15486 lines (15485 with data), 509.2 kB
{
"cells": [
{
"cell_type": "code",
"execution_count": 34,
"metadata": {},
"outputs": [],
"source": [
"from __future__ import print_function\n",
"import pandas as pd\n",
"import os,sys\n",
"import pybedtools as pbt\n",
"from StringIO import StringIO\n",
"import matplotlib.pyplot as plt\n",
"import seaborn as sns\n",
"import numpy as np\n",
"import re\n",
"from mapper import expand, parse_mapping_table, apply_mappers\n",
"\n",
"root_dir = \"/home/olya/SFU/Hossein/v2/\"\n",
"preprocessed_dir = root_dir+\"preprocessed/mutations/\"\n",
"w = 0.05\n",
"%matplotlib inline"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Converting mutations to gene-level score (-1;1)\n",
"* differentiate TSG and OG\n",
" \n",
" We use two lists of TSG and OG and their driver mutations obtained from OncoKB:\n",
" \n",
"\n",
"* differentiate mutations by their potential effect\n",
" \n",
" We take into consideration a protential effect of all mutations in every altered gene proposed based on \n",
" - type of protein change\n",
" - proximity to known driver mutations\n",
"\n",
"#### TSG potential loss-of-function \n",
" *-1 if any truncating variant found \n",
" *-1/(x+1) if any variant found at the distance x of database LoF\n",
"#### OG potential gain-of-function \n",
" * +1 if any variant match the position of database GoF variant \n",
" * +1/(x+1) if any variant found at the distance x of database GoF\n",
" * However, some genes annotated as TSG and OG in COSMIC. If such a gene has a truncating variant, it gets -1. If such gene has a truncating variant, we exclude it from the consideration. \n",
" * Many OG are activated via overexpression or apmplification, but not via somatic mutations. We exclude such OG from consideration, because it is impossible to propose the effect of a mutation in such OGs. Every OG has at least one mutation\n",
" \n",
"### Sources of mutations\n",
"We need:\n",
" * a list of genes labelled as TSG or OG \n",
" * a list of driver mutations or hotspots with protein coordinates \n",
" \n",
"1). COSMIC CGC - 1). list of driver genes, classified as TSG, OG or fusions; Tiers 1 and 2 2). list of mutations in these genes in every sample included in COSMIC\n",
"\n",
"2). OncoKB - curated list of 1) driver genes and 2) mutations with effects.\n",
"\n",
"3). Bailey et al. 2018 Cell \"Comprehensive Characterization\n",
"of Cancer Driver Genes and Mutation\" - they report only driver genes with any mutations or hotspots. \n",
"\n",
"4). Iorio et al. 2016 - \n",
"\n",
"5). cBioPortal - 1D https://www.cancerhotspots.org and 3D hotspots https://www.3dhotspots.org.\n",
"\n",
"\n",
"# Workflow\n",
"\n",
"1). Mutations - union of 1D and 3D hotspots \n",
"2). List of genes:\n",
" * TSG: union of Bailey et al. 2018 and OncoKB\n",
" * OG: genes from union of Bailey et al., 2018 and OncoKB OG lists which had any mutation hotspot\n",
"3). Mutation classification by effect on protein:\n",
" * potential LoF: frameshift,nonsense,ess_splice,stop_lost\n",
" * potential GoF: missense, inframe indels\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": 35,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"OncoKB OG: 214 TSG: 246 OG_TSG: 25\n"
]
}
],
"source": [
"# from http://oncokb.org/#/cancerGenes\n",
"OncoKB_mut = pd.read_csv(\"../../hotspots/OncoKB/allAnnotatedVariants.tsv\",sep =\"\\t\")\n",
"OncoKB_gtype = pd.read_csv(\"../../hotspots/OncoKB/OncoKB_gene_type.txt\",sep =\"\\t\")\n",
"OncoKB_gtype = OncoKB_gtype[['Hugo Symbol ', u'Oncogene /TSG ']]\n",
"OncoKB = {\"OG\":'Oncogene ',\"TSG\":'TSG ',\"OG_TSG\":'Oncogene,TSG '}\n",
"for key in OncoKB.keys():\n",
" OncoKB[key] = set(map(str.rstrip, list(set(OncoKB_gtype.loc[OncoKB_gtype['Oncogene /TSG ']== OncoKB[key],'Hugo Symbol '].values))))\n",
"\n",
"OncoKB[\"OG\"].update(OncoKB[\"OG_TSG\"])\n",
"OncoKB[\"TSG\"].update(OncoKB[\"OG_TSG\"]) \n",
"print(\"OncoKB OG:\",len(OncoKB[\"OG\"]),\"TSG:\",len(OncoKB[\"TSG\"]),\"OG_TSG:\",len(OncoKB[\"OG_TSG\"]))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Algorithm:\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": 36,
"metadata": {},
"outputs": [],
"source": [
"# gene_id - Entrez Gene ID \n",
"# df - all mutations in sample\n",
"# columns: \"aa_pos\",\"function\", \"Entrez_gene_ID\"\n",
"# hotspots - table of known hotsport \"Entrez_gene_ID\" and \"aa_pos\"\n",
"\n",
"def distance_to_hotspot(gene_id,df_gene, hotspots):\n",
" '''Returns minimal distance between point mutation in gene and known hotspot'''\n",
" # consider only GoF because LoF affect the whole protein and not a certian point\n",
" df_gene = df_gene.loc[df_gene[\"function\"] == \"point_mutation\"]\n",
" df_hotspots = hotspots.loc[hotspots[\"Entrez_gene_ID\"] == gene_id, :]\n",
" dist = 100000\n",
" for s,e in set(df_gene[\"aa_pos\"].values):\n",
" for hs, he in set(df_hotspots[\"aa_pos\"].values):\n",
" dist = min(dist, abs(s-hs),abs(s-he), abs(e-hs), abs(e-he))\n",
" return dist\n",
"\n",
"def mutations2score(df,TSG,OG,hotspots, w=0.05,verbose = False):\n",
" # define gene type\n",
" gene_scores = {}\n",
" for gene_id in list(set(df[\"Entrez_gene_ID\"].values)):\n",
" df_gene = df.loc[df[\"Entrez_gene_ID\"] == gene_id, :]\n",
" # functions of mutations\n",
" mut_functions = set(df_gene[\"function\"].values)\n",
" if gene_id in TSG:\n",
" # check for truncating mutations:\n",
" # score is -1 if any\n",
" if \"truncating_mutation\" in mut_functions:\n",
" gene_scores[gene_id] =-1\n",
" else:\n",
" # in mutation is not truncating, \n",
" # get the distance to closets hotspot if any \n",
" dist = distance_to_hotspot(gene_id, df_gene, hotspots)\n",
" # set abs. maximal of 1/(dist+1) and 2w which corresponds LoF in unannotatedd gene\n",
" gene_scores[gene_id] = -max(1.0/(dist+1),2*w)\n",
" elif gene_id in OG:\n",
" if \"point_mutation\" in mut_functions:\n",
" dist = distance_to_hotspot(gene_id, df_gene, hotspots)\n",
" if \"truncating_mutation\" in mut_functions:\n",
" if verbose:\n",
" print(\"GoF at dist\",dist,\"from hotspot in Oncogene with GoF\",file = sys.stderr)\n",
" print(df_gene,file = sys.stderr)\n",
" if 1.0/(dist+1) > 2*w:\n",
" # if there is a mutation close to hotspot\n",
" # despite LoF it is likely a driver and the second copy of this gene is broken\n",
" # this happens in sampl 905968 in PIK3CA gene (5290)\n",
" gene_scores[gene_id] = 1.0/(dist+1)\n",
" else:\n",
" # otherwise we set -1 to differentiate it from neutral mutations\n",
" # because oncogene might turn on after domain truncation\n",
" gene_scores[gene_id] = -1\n",
" else:\n",
" # non-hotspot mutation in non-LoF oncogene - small positive value\n",
" gene_scores[gene_id] = max(1.0/(dist+1),w)\n",
" else:\n",
" # only LoF mutations, oncogene is likely not functional or\n",
" # it is turned-on after truncting mutations\n",
" # therefore we set -1 to differentiate it from neutral mutations\n",
" gene_scores[gene_id] = -1\n",
" \n",
" \n",
" else: # if unknown_significance\n",
" if \"truncating_mutation\" in mut_functions:\n",
" gene_scores[gene_id] = -2.0*w\n",
" else:\n",
" gene_scores[gene_id] = -w\n",
" \n",
" return pd.Series(gene_scores)"
]
},
{
"cell_type": "code",
"execution_count": 37,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Bailey_2018 OG: 115 TSG: 162 both: 18\n"
]
}
],
"source": [
"bailye = {\"OG\":[],\"TSG\":[],\"OG_TSG\":[]}\n",
"bailye_drivers = pd.read_excel(\"../../hotspots/Bailey_2018.mmc1.xlsx\", sheet_name=\"Table S1\", \n",
" skiprows = 3)\n",
"bailye_drivers = bailye_drivers[[\"Gene\",\"Tumor suppressor or oncogene prediction (by 20/20+)\"]]\n",
"#print(bailye_drivers.shape[0])\n",
"bailye_drivers.drop_duplicates(inplace=True)\n",
"bailye_drivers.columns = [\"gene\", \"role\"]\n",
"#print(bailye_drivers.shape[0])\n",
"bailye_drivers.fillna(\"NA\", inplace = True)\n",
"bailye_drivers[\"role\"] = bailye_drivers[\"role\"].apply(lambda x: x.replace(\"possible \",\"\"))\n",
"bailye_drivers.drop_duplicates(inplace=True)\n",
"#print(bailye_drivers.shape[0])\n",
"bailye_drivers.loc[bailye_drivers.duplicated(\"gene\", keep=False),:]\n",
"#print(len(set(bailye_drivers[\"gene\"].values)))\n",
"bailye[\"OG\"] = bailye_drivers.loc[bailye_drivers[\"role\"] == \"oncogene\",:]\n",
"bailye[\"OG\"] = set(bailye[\"OG\"][\"gene\"].values)\n",
"bailye[\"TSG\"] = bailye_drivers.loc[bailye_drivers[\"role\"] == \"tsg\",:]\n",
"bailye[\"TSG\"] = set(bailye[\"TSG\"][\"gene\"].values)\n",
"bailye[\"OG_TSG\"] = bailye[\"OG\"].intersection(bailye[\"TSG\"])\n",
"print(\"Bailey_2018 OG:\",len(bailye[\"OG\"]),\"TSG:\",len(bailye[\"TSG\"]),\"both:\", len(bailye[\"OG_TSG\"]))\n",
"#print(len(OncoKB[\"OG\"]),len(OncoKB[\"TSG\"]),len(OncoKB[\"OG_TSG\"]) ) "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Hotspots "
]
},
{
"cell_type": "code",
"execution_count": 38,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"1D mutations 3004 495\n",
"1D hotspots 1024 55\n",
"3D mutations 9512\n",
"3D hotspots 3395\n",
"genes with hotspot 688\n",
"unique hotspots 4258\n"
]
}
],
"source": [
"hotspots2D_subst = pd.read_excel(\"../../hotspots/hotspots_v2.xls\",\"24K_hotspots_cancerhotspots-org_singlecodon\")\n",
"hotspots2D_indels = pd.read_excel(\"../../hotspots/hotspots_v2.xls\",\"24K_hotspots_cancerhotspots-org_indels\")\n",
"print(\"1D mutations\",hotspots2D_subst.shape[0],hotspots2D_indels.shape[0] )\n",
"hotspots2D_subst = hotspots2D_subst.loc[~hotspots2D_subst[\"Amino_Acid_Position\"].str.contains(\"splice\")]\n",
"hotspots2D_subst = hotspots2D_subst[[\"Hugo_Symbol\",\"Amino_Acid_Position\"]]\n",
"hotspots2D_subst.drop_duplicates(inplace=True)\n",
"hotspots2D_indels = hotspots2D_indels[[\"Hugo_Symbol\",\"Amino_Acid_Position\"]]\n",
"hotspots2D_indels.drop_duplicates(inplace=True)\n",
"print(\"1D hotspots\",hotspots2D_subst.shape[0],hotspots2D_indels.shape[0] )\n",
"cBioPortal_muts = pd.concat([hotspots2D_subst,hotspots2D_indels],axis =0)\n",
"cBioPortal_muts_ = cBioPortal_muts.loc[cBioPortal_muts[\"Amino_Acid_Position\"].str.contains(\"-\"),:]\n",
"cBioPortal_muts = cBioPortal_muts.loc[~cBioPortal_muts[\"Amino_Acid_Position\"].str.contains(\"-\"),:]\n",
"cBioPortal_muts[\"Amino_Acid_Position\"] = cBioPortal_muts[\"Amino_Acid_Position\"].apply(int)\n",
"#cBioPortal_muts[\"start\"] = cBioPortal_muts[\"Amino_Acid_Position\"]\n",
"#cBioPortal_muts[\"end\"] = cBioPortal_muts[\"Amino_Acid_Position\"]\n",
"cBioPortal_muts[\"aa_pos\"] = cBioPortal_muts[\"Amino_Acid_Position\"].apply(lambda x : (x,x))\n",
"\n",
"#cBioPortal_muts_ [\"start\"] = cBioPortal_muts_[\"Amino_Acid_Position\"].apply(lambda x: int(x.split(\"-\")[0]))\n",
"#cBioPortal_muts_[\"end\"] = cBioPortal_muts_[\"Amino_Acid_Position\"].apply(lambda x: int(x.split(\"-\")[1]))\n",
"cBioPortal_muts_[\"aa_pos\"] = cBioPortal_muts_[\"Amino_Acid_Position\"].apply(lambda x : tuple(map(int,x.split(\"-\"))))\n",
"\n",
"cBioPortal_muts = pd.concat([cBioPortal_muts_,cBioPortal_muts],axis = 0)\n",
"cBioPortal_muts[\"source\"] = \"1D\"\n",
"\n",
"\n",
"### 3D\n",
"\n",
"cBioPortal_3D = pd.read_excel(\"../../hotspots/3d_hotspots.xls\",\"Table S5\")\n",
"cBioPortal_3D = cBioPortal_3D[[\"Gene\",\"Amino_Acid_Position\"]]\n",
"print(\"3D mutations\",cBioPortal_3D.shape[0])\n",
"cBioPortal_3D.drop_duplicates(inplace=True)\n",
"print(\"3D hotspots \",cBioPortal_3D.shape[0])\n",
"cBioPortal_3D[\"Amino_Acid_Position\"] = cBioPortal_3D[\"Amino_Acid_Position\"].apply(int)\n",
"#cBioPortal_3D[\"start\"] = cBioPortal_3D[\"Amino_Acid_Position\"]\n",
"#cBioPortal_3D[\"end\"] = cBioPortal_3D[\"Amino_Acid_Position\"]\n",
"cBioPortal_3D[\"aa_pos\"] = cBioPortal_3D[\"Amino_Acid_Position\"].apply(lambda x : (x,x))\n",
"cBioPortal_3D.rename({\"Gene\":'Hugo_Symbol'}, axis=\"columns\",inplace=True)\n",
"cBioPortal_3D[\"source\"] = \"3D\"\n",
"cBioPortal_muts = cBioPortal_muts[[\"Hugo_Symbol\",\"aa_pos\"]]\n",
"cBioPortal_3D = cBioPortal_3D[[\"Hugo_Symbol\",\"aa_pos\"]]\n",
"cBioPortal_muts = pd.concat([cBioPortal_3D, cBioPortal_muts],axis=0)\n",
"cBioPortal_muts.sort_values([\"Hugo_Symbol\"],ascending = True,inplace=True)\n",
"\n",
"cBioPortal_genes = set(cBioPortal_muts[\"Hugo_Symbol\"].values)\n",
"print(\"genes with hotspot\",len(cBioPortal_genes))\n",
"cBioPortal_muts = cBioPortal_muts[[\"Hugo_Symbol\",\"aa_pos\"]]\n",
"cBioPortal_muts.drop_duplicates(inplace=True)\n",
"print(\"unique hotspots\",cBioPortal_muts.shape[0])\n",
"#cBioPortal_muts"
]
},
{
"cell_type": "code",
"execution_count": 39,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"genes with and without mutations\n",
"OG oncokb 110 / 214 Bailye_2018 81 / 115\n",
"TSG oncokb 123 / 246 Bailye_2018 81 / 162\n",
"OG_TSG oncokb 15 / 25 Bailye_2018 14 / 18\n"
]
}
],
"source": [
"print(\"genes with and without mutations\")\n",
"for kind in [\"OG\",\"TSG\",\"OG_TSG\"]:\n",
" oncokb = OncoKB[kind].intersection(cBioPortal_genes) \n",
" b = bailye[kind].intersection(cBioPortal_genes)\n",
" print(kind,\"oncokb\", len(oncokb),\"/\",len(OncoKB[kind]),\n",
" \"Bailye_2018\", len(b),\"/\",len(bailye[kind]))"
]
},
{
"cell_type": "code",
"execution_count": 40,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"OG oncokb 214 Bailye_2018 115 union 277 mutated: 144\n",
"TSG oncokb 246 Bailye_2018 162 union 316 mutated: 136\n",
"OG_TSG oncokb 25 Bailye_2018 18 union 41 mutated: 28\n"
]
}
],
"source": [
"for kind in [\"OG\",\"TSG\",\"OG_TSG\"]:\n",
" oncokb = OncoKB[kind]#.intersection(cBioPortal_genes) \n",
" b = bailye[kind]#.intersection(cBioPortal_genes)\n",
" print(kind,\"oncokb\", len(oncokb),\n",
" \"Bailye_2018\", len(b),\"union\",len(b.union(oncokb)),\n",
" \"mutated:\",\n",
" len(b.union(oncokb).intersection(cBioPortal_genes)))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"TSG: 316 with hotspots: 136 \n",
"OG with hotspots: 144\n",
"Hotspots (all from cBioPortal): 4258 \n",
"\ton OG: 1116 \n",
"\ton TSG: 1012\n"
]
},
{
"data": {
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" text-align: right;\n",
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Hugo_Symbol</th>\n",
" <th>aa_pos</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>1456</th>\n",
" <td>ACVR1</td>\n",
" <td>(206, 206)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1307</th>\n",
" <td>ACVR1</td>\n",
" <td>(258, 258)</td>\n",
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" <th>1128</th>\n",
" <td>ACVR1</td>\n",
" <td>(328, 328)</td>\n",
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" <tr>\n",
" <th>2542</th>\n",
" <td>ACVR1B</td>\n",
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" <th>2056</th>\n",
" <td>ACVR1B</td>\n",
" <td>(401, 401)</td>\n",
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],
"text/plain": [
" Hugo_Symbol aa_pos\n",
"1456 ACVR1 (206, 206)\n",
"1307 ACVR1 (258, 258)\n",
"1128 ACVR1 (328, 328)\n",
"2542 ACVR1B (398, 398)\n",
"2056 ACVR1B (401, 401)"
]
},
"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# TSG - not necessarity with a hotspot, take union of OncoKB and Bailye_2018\n",
"TSG = OncoKB[\"TSG\"].union(bailye[\"TSG\"])\n",
"# OG - must have a hotspot \n",
"OG = OncoKB[\"OG\"].union(bailye[\"OG\"]).intersection(cBioPortal_genes)\n",
"print(\"TSG:\",len(TSG),\"with hotspots:\",len(TSG.intersection(cBioPortal_genes)),\n",
" \"\\nOG with hotspots:\",len(OG))\n",
"# list of hotspots: \n",
"hotspots = cBioPortal_muts.loc[cBioPortal_muts[\"Hugo_Symbol\"].isin(OG|TSG),:]\n",
"print(\"Hotspots (all from cBioPortal):\", cBioPortal_muts.shape[0],\n",
" \"\\n\\ton OG:\", hotspots.loc[hotspots[\"Hugo_Symbol\"].isin(OG)].shape[0],\n",
" \"\\n\\ton TSG:\", hotspots.loc[hotspots[\"Hugo_Symbol\"].isin(TSG)].shape[0])\n",
"hotspots.head(5)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### map gene name to Entrez gene ID "
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Ok: no empty rows detected\n",
"Ok: no duplicated pairs detected\n",
"Ok: All Symbol rows are not empty.\n",
"Ok: All Symbol are mapped to GeneID\n",
"16 Symbol mapped to multiple GeneID\n",
"Ok: All GeneID are unique\n",
"59266 Symbol can be mapped directly to GeneID\n"
]
}
],
"source": [
"NCBI = pd.read_csv(root_dir+\"Homo_sapiens.gene_info\",sep = \"\\t\")\n",
"NCBI = NCBI[[\"#tax_id\",\"GeneID\",\"Symbol\",\"Synonyms\",\"type_of_gene\"]]\n",
"NCBI = NCBI.loc[NCBI[\"#tax_id\"] == 9606]\n",
"NCBI = NCBI.loc[NCBI[\"type_of_gene\"] != \"unknown\"]\n",
"ncbi_symbols = parse_mapping_table(NCBI, \"Symbol\",\"GeneID\")"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Ok: no empty rows detected\n",
"Ok: no duplicated pairs detected\n",
"Ok: All Synonyms rows are not empty.\n",
"Ok: All Synonyms are mapped to GeneID\n",
"3145 Synonyms mapped to multiple GeneID\n",
"49179 different Synonyms mapped to the same GeneID\n",
"10839 Synonyms can be mapped directly to GeneID\n"
]
}
],
"source": [
"ncbi_synonyms = expand(NCBI[[\"Synonyms\",\"GeneID\"]],column=\"Synonyms\",sep=\"|\") \n",
"ncbi_synonyms = parse_mapping_table(ncbi_synonyms, \"Synonyms\",\"GeneID\")"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Mapped: 421 \n",
"\tdirectly via main_mapper 414 \n",
"\tvia alternative mapper 2 \n",
"\tvia one of multiple synonyms in alternative mapper 5 \n",
"\tLOC 0 \n",
"Unmapped: 0 \n",
"\trecognized symbols without Entrez ID 0 \n",
"\tmultiple query_ids map to the same target_id 0 \n",
"\tquery_ids map to multiple target_ids in the main mapper 0 \n",
"\tquery_ids map to multiple target_ids in the alternative mapper 0 \n",
"\tLOC not found in Entrez 0 \n",
"\tNot found at all: 0\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"IDs mapped to multiple target IDs are kept:\n",
" []\n",
"/home/olya/miniconda2/lib/python2.7/site-packages/ipykernel_launcher.py:5: SettingWithCopyWarning: \n",
"A value is trying to be set on a copy of a slice from a DataFrame.\n",
"Try using .loc[row_indexer,col_indexer] = value instead\n",
"\n",
"See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n",
" \"\"\"\n"
]
},
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Hugo_Symbol</th>\n",
" <th>aa_pos</th>\n",
" <th>Entrez_gene_ID</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>1456</th>\n",
" <td>ACVR1</td>\n",
" <td>(206, 206)</td>\n",
" <td>90</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1307</th>\n",
" <td>ACVR1</td>\n",
" <td>(258, 258)</td>\n",
" <td>90</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1128</th>\n",
" <td>ACVR1</td>\n",
" <td>(328, 328)</td>\n",
" <td>90</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2542</th>\n",
" <td>ACVR1B</td>\n",
" <td>(398, 398)</td>\n",
" <td>91</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2056</th>\n",
" <td>ACVR1B</td>\n",
" <td>(401, 401)</td>\n",
" <td>91</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" Hugo_Symbol aa_pos Entrez_gene_ID\n",
"1456 ACVR1 (206, 206) 90\n",
"1307 ACVR1 (258, 258) 90\n",
"1128 ACVR1 (328, 328) 90\n",
"2542 ACVR1B (398, 398) 91\n",
"2056 ACVR1B (401, 401) 91"
]
},
"execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"tsg_og_gene_names = pd.DataFrame.from_dict({\"genes\":dict(zip(list(OG | TSG),list(OG | TSG)))})\n",
"tsg_og_gene_names, query2target, not_mapped = apply_mappers(tsg_og_gene_names, ncbi_symbols, ncbi_synonyms, verbose = True,handle_duplicates = \"keep\")\n",
"OG_entrez = set(map(lambda x : query2target[x],OG))\n",
"TSG_entrez = set(map(lambda x : query2target[x],TSG))\n",
"hotspots[\"Entrez_gene_ID\"] = hotspots[\"Hugo_Symbol\"].apply(lambda x : query2target[x])\n",
"hotspots.head()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# GDSC mutations \n",
"ID, cDNA and aa coordinates; sometimes gene name is Ensembl 56 ID, sometimes HGNC. When map gene names to current Entrez gene IDs, many important genes like MLL2 and MLL4 ambiguously renamed as KMT2D and KMT2B or vise versa are lost. \n",
"https://en.wikipedia.org/wiki/KMT2D\n",
"\n",
" Only protein coding mutations reported; of them: \n",
" * potential LoF : 'frameshift','nonsense','stop_lost','ess_splice'\n",
" * potential GoF : 'missense','Missense','inframe'\n",
" * 'gene_fusion' records exluded because they do not correspond to a point mutation and present not in all datasets. Although most of recurrent fusions are GoF, some may be LoF (PMC4889949)\n",
" \n",
"wget ftp.sanger.ac.uk/pub/project/cancerrxgene/releases/release-7.0/ WES_variants.xlsx."
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>COSMIC_ID</th>\n",
" <th>Gene</th>\n",
" <th>AA</th>\n",
" <th>Classification</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>907272</td>\n",
" <td>A1BG</td>\n",
" <td>p.Y281C</td>\n",
" <td>missense</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>998184</td>\n",
" <td>A1BG</td>\n",
" <td>p.A197T</td>\n",
" <td>missense</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>907272</td>\n",
" <td>A1BG</td>\n",
" <td>p.A191T</td>\n",
" <td>missense</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" COSMIC_ID Gene AA Classification\n",
"0 907272 A1BG p.Y281C missense\n",
"1 998184 A1BG p.A197T missense\n",
"2 907272 A1BG p.A191T missense"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"gdsc = pd.read_excel(\"/home/olya/SFU/Hossein/GDSC/WES_variants.xlsx\",\"WES_variants\")\n",
"gdsc = gdsc [[\"COSMIC_ID\",\"Gene\",\"AA\",\"Classification\"]]\n",
"gdsc.head(3)\n"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Classification\n",
"missense 413252\n",
"frameshift 31933\n",
"nonsense 23359\n",
"ess_splice 13106\n",
"inframe 3185\n",
"Missense 884\n",
"stop_lost 486\n",
"gene_fusion 38\n",
"dtype: int64"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"gdsc.groupby(\"Classification\").size().sort_values(ascending = False)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"mean 485.7 median 288.0\n"
]
},
{
"data": {
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\n",
"text/plain": [
"<Figure size 1440x360 with 2 Axes>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"# define functional effect of a mutation \n",
"gdsc_truncating = ['frameshift','nonsense','stop_lost','ess_splice']\n",
"gdsc_point = ['missense','Missense','inframe']\n",
"gdsc.loc[gdsc[\"Classification\"].isin(gdsc_truncating),\"function\"] = \"truncating_mutation\"\n",
"gdsc.loc[gdsc[\"Classification\"].isin(gdsc_point),\"function\"] = \"point_mutation\"\n",
"gdsc = gdsc.loc[gdsc[\"Classification\"].isin(gdsc_truncating+gdsc_point),:]\n",
"\n",
"plt.figure(figsize=(20,5))\n",
"plt.subplot(1,2,1)\n",
"n_mutations_gdsc = gdsc.groupby(\"COSMIC_ID\").size().sort_values(ascending = False)\n",
"tmp = plt.hist(n_mutations_gdsc, bins=50,range = (0,2000))\n",
"tmp = plt.title(\"number of mutations per sample in GDSC\")\n",
"ax = plt.subplot(1,2,2)\n",
"n_LoF = gdsc.loc[gdsc[\"Classification\"].isin(gdsc_truncating ),:].groupby(\"COSMIC_ID\").size().sort_values(ascending = False)\n",
"n_GoF = gdsc.loc[gdsc[\"Classification\"].isin(gdsc_point),:].groupby(\"COSMIC_ID\").size().sort_values(ascending = False)\n",
"df = pd.DataFrame.from_dict({\"truncating_mutations\":n_LoF,\"point_mutations\":n_GoF})\n",
"#tmp = plt.hist(n_LoF, bins=50)\n",
"#tmp = plt.title(\"LoF mutations per sample in GDSC\")\n",
"df.plot.hist(stacked = True, bins = 50,ax =ax,range = (0,2000))\n",
"print(\"mean\",round(np.mean(n_mutations_gdsc),1), \"median\",np.median(n_mutations_gdsc))\n"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {},
"outputs": [],
"source": [
"def binarize(x):\n",
" if x==0:\n",
" return x\n",
" else:\n",
" return 1\n",
"\n",
"def get_aa_pos_GDSC(x):\n",
" l = re.findall(r'\\d+', x)\n",
" if len(l) == 0:\n",
" #print(x, \"positions not found.\",file = sys.stderr)\n",
" return (\"NA\",\"NA\")\n",
" elif len(l) == 1:\n",
" return (int(l[0]), int(l[0]))\n",
" else:\n",
" return (int(l[0]), int(l[1]))"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
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" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>COSMIC_ID</th>\n",
" <th>Gene</th>\n",
" <th>AA</th>\n",
" <th>Classification</th>\n",
" <th>function</th>\n",
" <th>aa_pos</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>907272</td>\n",
" <td>A1BG</td>\n",
" <td>p.Y281C</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>(281, 281)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>998184</td>\n",
" <td>A1BG</td>\n",
" <td>p.A197T</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>(197, 197)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>907272</td>\n",
" <td>A1BG</td>\n",
" <td>p.A191T</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>(191, 191)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>907289</td>\n",
" <td>A1BG</td>\n",
" <td>p.D486N</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>(486, 486)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>905989</td>\n",
" <td>A1BG</td>\n",
" <td>p.T257N</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>(257, 257)</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" COSMIC_ID Gene AA Classification function aa_pos\n",
"0 907272 A1BG p.Y281C missense point_mutation (281, 281)\n",
"1 998184 A1BG p.A197T missense point_mutation (197, 197)\n",
"2 907272 A1BG p.A191T missense point_mutation (191, 191)\n",
"3 907289 A1BG p.D486N missense point_mutation (486, 486)\n",
"4 905989 A1BG p.T257N missense point_mutation (257, 257)"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"\n",
"gdsc[\"aa_pos\"] = gdsc[\"AA\"].apply(lambda x : get_aa_pos_GDSC(x))\n",
"#gdsc[\"start\"] = gdsc[\"aa_pos\"].apply(lambda x : x.split(\",\")[0])\n",
"#gdsc[\"end\"] = gdsc[\"aa_pos\"].apply(lambda x : x.split(\",\")[1])\n",
"gdsc.head(5)"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"ENSEMBL gene IDs found: 101\n",
"Gene symbols: 18989\n"
]
}
],
"source": [
"ensg_genes = []\n",
"symbols = []\n",
"for gene in set(gdsc[\"Gene\"].values):\n",
" if gene.startswith(\"ENSG\"):\n",
" ensg_genes.append(gene)\n",
" \n",
" else:\n",
" symbols.append(gene)\n",
"print(\"ENSEMBL gene IDs found:\",len(ensg_genes))\n",
"ensg_genes = gdsc.loc[gdsc[\"Gene\"].isin(ensg_genes), :]\n",
"gdsc_hugo = gdsc.loc[gdsc[\"Gene\"].isin(symbols), :]\n",
"print(\"Gene symbols:\",len(set(gdsc_hugo[\"Gene\"].values)))"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Mapped: 18509 \n",
"\tdirectly via main_mapper 17003 \n",
"\tvia alternative mapper 452 \n",
"\tvia one of multiple synonyms in alternative mapper 1029 \n",
"\tLOC 25 \n",
"Unmapped: 480 \n",
"\trecognized symbols without Entrez ID 0 \n",
"\tmultiple query_ids map to the same target_id 0 \n",
"\tquery_ids map to multiple target_ids in the main mapper 0 \n",
"\tquery_ids map to multiple target_ids in the alternative mapper 51 \n",
"\tLOC not found in Entrez 11 \n",
"\tNot found at all: 418\n",
"Warning: query IDs mapping to duplicated target IDs in mapping table: 174\n",
"Warning: query IDs not mapped to any target IDs excluded: 480\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/pandas/core/frame.py:3781: SettingWithCopyWarning: \n",
"A value is trying to be set on a copy of a slice from a DataFrame\n",
"\n",
"See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n",
" return super(DataFrame, self).rename(**kwargs)\n",
"IDs mapped to multiple target IDs are kept:\n",
" [143872, 23272, 341019, 27177, 387119, 84530, 26165, 11321, 122945, 150082, 2122, 442444, 79949, 157777, 340578, 100289124, 8805, 127602, 387707, 728194, 345222, 84108, 91283, 84631, 388761, 4253, 163486, 54438, 92017, 283310, 84148, 57018, 284352, 5315, 283849, 339669, 119016, 340204, 64753, 64760, 25849, 286464, 129285, 4360, 10507, 4883, 23334, 114984, 256815, 23345, 57662, 165186, 93081, 54617, 84316, 200030, 10592, 57705, 246126, 126321, 10613, 374, 79741, 51586, 144535, 728642, 168850, 647060, 284565, 63895, 201625, 29086, 1954, 9127, 29099, 941, 155066, 140733, 85452, 139728, 84458, 55719, 23028, 245913, 54777, 79868]\n",
"mapper.py:204: SettingWithCopyWarning: \n",
"A value is trying to be set on a copy of a slice from a DataFrame\n",
"\n",
"See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n",
" df.sort_index(inplace=True)\n"
]
}
],
"source": [
"# mapping to Entrez\n",
"df = gdsc_hugo[[\"Gene\"]].copy()\n",
"df.set_index(\"Gene\",drop= False ,inplace=True)\n",
"df.drop_duplicates(inplace = True)\n",
"df, query2target,not_mapped = apply_mappers(df, ncbi_symbols, ncbi_synonyms, verbose = True,handle_duplicates = \"keep\")"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"data": {
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" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>COSMIC_ID</th>\n",
" <th>Gene</th>\n",
" <th>AA</th>\n",
" <th>Classification</th>\n",
" <th>function</th>\n",
" <th>aa_pos</th>\n",
" <th>Entrez_gene_ID</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>907272</td>\n",
" <td>A1BG</td>\n",
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" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>(281, 281)</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>998184</td>\n",
" <td>A1BG</td>\n",
" <td>p.A197T</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>(197, 197)</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>907272</td>\n",
" <td>A1BG</td>\n",
" <td>p.A191T</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>(191, 191)</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>907289</td>\n",
" <td>A1BG</td>\n",
" <td>p.D486N</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>(486, 486)</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>905989</td>\n",
" <td>A1BG</td>\n",
" <td>p.T257N</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>(257, 257)</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>909698</td>\n",
" <td>A1BG</td>\n",
" <td>p.R90H</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>(90, 90)</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>905971</td>\n",
" <td>A1BG</td>\n",
" <td>p.T46M</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>(46, 46)</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>909761</td>\n",
" <td>A1BG</td>\n",
" <td>p.P41fs*33</td>\n",
" <td>frameshift</td>\n",
" <td>truncating_mutation</td>\n",
" <td>(41, 33)</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>1327769</td>\n",
" <td>A1BG</td>\n",
" <td>p.E249D</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>(249, 249)</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>1330931</td>\n",
" <td>A1BG</td>\n",
" <td>p.Y184*</td>\n",
" <td>nonsense</td>\n",
" <td>truncating_mutation</td>\n",
" <td>(184, 184)</td>\n",
" <td>1</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" COSMIC_ID Gene AA Classification function \\\n",
"0 907272 A1BG p.Y281C missense point_mutation \n",
"1 998184 A1BG p.A197T missense point_mutation \n",
"2 907272 A1BG p.A191T missense point_mutation \n",
"3 907289 A1BG p.D486N missense point_mutation \n",
"4 905989 A1BG p.T257N missense point_mutation \n",
"5 909698 A1BG p.R90H missense point_mutation \n",
"6 905971 A1BG p.T46M missense point_mutation \n",
"7 909761 A1BG p.P41fs*33 frameshift truncating_mutation \n",
"8 1327769 A1BG p.E249D missense point_mutation \n",
"9 1330931 A1BG p.Y184* nonsense truncating_mutation \n",
"\n",
" aa_pos Entrez_gene_ID \n",
"0 (281, 281) 1 \n",
"1 (197, 197) 1 \n",
"2 (191, 191) 1 \n",
"3 (486, 486) 1 \n",
"4 (257, 257) 1 \n",
"5 (90, 90) 1 \n",
"6 (46, 46) 1 \n",
"7 (41, 33) 1 \n",
"8 (249, 249) 1 \n",
"9 (184, 184) 1 "
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"gdsc_hugo = gdsc_hugo.loc[~gdsc_hugo[\"Gene\"].isin(not_mapped),:].copy()\n",
"gdsc_hugo[\"Entrez_gene_ID\"] = gdsc_hugo[\"Gene\"].apply(lambda x : query2target[x])\n",
"gdsc_hugo.head(10)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {
"scrolled": true
},
"outputs": [
{
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],
"text/plain": [
" 683665 683667 684052 684055 684057 684059 684062 684072 \\\n",
"7157 0.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 -1.0 \n",
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"4893 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 \n",
"\n",
" 684681 687448 ... 1659818 1659819 1659823 1659928 1659929 \\\n",
"7157 0.0 0.0 ... 0.0 -1.0 -1.0 0.0 0.0 \n",
"5290 0.0 0.0 ... 0.0 0.0 -1.0 0.0 0.0 \n",
"3845 0.0 0.0 ... 1.0 0.0 0.0 1.0 0.0 \n",
"4893 0.0 0.0 ... 0.0 0.0 0.0 0.0 0.0 \n",
"\n",
" 1660034 1660035 1660036 1674021 1789883 \n",
"7157 -1.0 -1.0 -1.00 -1.0 -1.0 \n",
"5290 1.0 0.0 0.05 1.0 0.0 \n",
"3845 1.0 1.0 1.00 0.0 0.0 \n",
"4893 0.0 0.0 -0.10 0.0 0.0 \n",
"\n",
"[4 rows x 1001 columns]"
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"gdsc_scores = {}\n",
"for sample in list(set(gdsc_hugo[\"COSMIC_ID\"].values)):\n",
" df = gdsc_hugo.loc[gdsc_hugo[\"COSMIC_ID\"] == sample,:]\n",
" gdsc_scores[sample] = mutations2score(df, TSG_entrez,OG_entrez, hotspots, w=w)\n",
"gdsc_scores = pd.DataFrame.from_dict(gdsc_scores)\n",
"gdsc_scores.fillna(0,inplace=True)\n",
"#import seaborn as sns\n",
"#sns.heatmap(gdsc_scores.loc[[7157,5290,3845,2312,4893],:])\n",
"gdsc_scores.to_csv(preprocessed_dir+\"/GDSC.non_bin_mutations.tsv\",sep = \"\\t\")\n",
"gdsc_scores.loc[[7157,5290,3845,4893],:]"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
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" <th>684055</th>\n",
" <th>684057</th>\n",
" <th>684059</th>\n",
" <th>684062</th>\n",
" <th>684072</th>\n",
" <th>684681</th>\n",
" <th>687448</th>\n",
" <th>...</th>\n",
" <th>1659818</th>\n",
" <th>1659819</th>\n",
" <th>1659823</th>\n",
" <th>1659928</th>\n",
" <th>1659929</th>\n",
" <th>1660034</th>\n",
" <th>1660035</th>\n",
" <th>1660036</th>\n",
" <th>1674021</th>\n",
" <th>1789883</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>7157</th>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>...</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5290</th>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>...</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3845</th>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>...</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2312</th>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>...</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4893</th>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>...</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>5 rows × 1001 columns</p>\n",
"</div>"
],
"text/plain": [
" 683665 683667 684052 684055 684057 684059 684062 684072 \\\n",
"7157 0.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 \n",
"5290 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 \n",
"3845 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 \n",
"2312 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 \n",
"4893 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 \n",
"\n",
" 684681 687448 ... 1659818 1659819 1659823 1659928 1659929 \\\n",
"7157 0.0 0.0 ... 0.0 1.0 1.0 0.0 0.0 \n",
"5290 0.0 0.0 ... 0.0 0.0 1.0 0.0 0.0 \n",
"3845 0.0 0.0 ... 1.0 0.0 0.0 1.0 0.0 \n",
"2312 0.0 0.0 ... 1.0 0.0 1.0 1.0 0.0 \n",
"4893 0.0 0.0 ... 0.0 0.0 0.0 0.0 0.0 \n",
"\n",
" 1660034 1660035 1660036 1674021 1789883 \n",
"7157 1.0 1.0 1.0 1.0 1.0 \n",
"5290 1.0 0.0 1.0 1.0 0.0 \n",
"3845 1.0 1.0 1.0 0.0 0.0 \n",
"2312 1.0 1.0 1.0 0.0 0.0 \n",
"4893 0.0 0.0 1.0 0.0 0.0 \n",
"\n",
"[5 rows x 1001 columns]"
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"\n",
"gdsc_scores = gdsc_scores.applymap(lambda x: binarize(x))\n",
"gdsc_scores.to_csv(preprocessed_dir+\"/GDSC.binary_mutations.tsv\",sep = \"\\t\")\n",
"gdsc_scores.loc[[7157,5290,3845,2312,4893],:]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# PDX\n",
"\n",
" * gene amplifications,deletions and mutations are mixed in one file\n",
" * gene ID - Symobols\n",
" * some gene IDs converted to datetime format\n",
" * mutation types: MutKnownFunctional, MutLikelyFunctional, MutNovel. Although we failed to find an explanation of the categories. \n",
" * 146 duplicated muataion records found (removed)\n"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"(262091, 5)\n"
]
},
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Sample</th>\n",
" <th>Gene</th>\n",
" <th>Entrez</th>\n",
" <th>Category</th>\n",
" <th>Details</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>X-1004</td>\n",
" <td>A2LD1</td>\n",
" <td>87769</td>\n",
" <td>Amp5</td>\n",
" <td>5.74</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>X-1004</td>\n",
" <td>ABCA4</td>\n",
" <td>24</td>\n",
" <td>MutNovel</td>\n",
" <td>K1831N,0.550</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>X-1004</td>\n",
" <td>ABCC13</td>\n",
" <td>150000</td>\n",
" <td>Amp8</td>\n",
" <td>8</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>X-1004</td>\n",
" <td>ABHD13</td>\n",
" <td>84945</td>\n",
" <td>Amp5</td>\n",
" <td>6.06</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>X-1004</td>\n",
" <td>ABTB1</td>\n",
" <td>80325</td>\n",
" <td>Amp5</td>\n",
" <td>6.82</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" Sample Gene Entrez Category Details\n",
"0 X-1004 A2LD1 87769 Amp5 5.74\n",
"1 X-1004 ABCA4 24 MutNovel K1831N,0.550\n",
"2 X-1004 ABCC13 150000 Amp8 8\n",
"3 X-1004 ABHD13 84945 Amp5 6.06\n",
"4 X-1004 ABTB1 80325 Amp5 6.82"
]
},
"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pdx = pd.read_excel(root_dir + \"../PDX/nm.3954-S2.xlsx\",\"pdxe_mut_and_cn2\")\n",
"print(pdx.shape)\n",
"pdx.head(5)"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Category\n",
"Amp5 51450\n",
"Amp8 9629\n",
"Del0.8 77022\n",
"MutKnownFunctional 11002\n",
"MutLikelyFunctional 172\n",
"MutNovel 112816\n",
"dtype: int64"
]
},
"execution_count": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pdx.groupby(\"Category\").size()"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"(123844, 5)\n",
"67 gene IDs were converted to datetimes Excel.\n"
]
}
],
"source": [
"# remove CNA, drop duplicated records\n",
"pdx = pdx.loc[~pdx[\"Category\"].isin([\"Amp5\",\"Amp8\",\"Del0.8\"]),:]\n",
"pdx = pdx.drop_duplicates()\n",
"print(pdx.shape)\n",
"df_size = pdx.shape[0]\n",
"# datetime genes\n",
"datetimes = pdx[\"Gene\"].apply(lambda x : type(x) == unicode or type(x) == str)\n",
"datetimes = datetimes[~datetimes].index\n",
"pdx_ = pdx.loc[datetimes,:]\n",
"pdx_ = pdx_.loc[pdx_[\"Entrez\"]!=\"None\",:]\n",
"pdx_[\"Entrez_gene_ID\"] = pdx_[\"Entrez\"].apply(int)\n",
"pdx_[\"Gene\"] = pdx_[\"Gene\"].apply(str)\n",
"pdx = pdx.loc[~pdx.index.isin(datetimes),:]\n",
"print(df_size - pdx.shape[0],\"gene IDs were converted to datetimes Excel.\")\n",
"#pdx.head(5)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"mutated genes in PDX cohort 15214\n",
"Mapped: 15062 \n",
"\tdirectly via main_mapper 14107 \n",
"\tvia alternative mapper 249 \n",
"\tvia one of multiple synonyms in alternative mapper 624 \n",
"\tLOC 82 \n",
"Unmapped: 152 \n",
"\trecognized symbols without Entrez ID 0 \n",
"\tmultiple query_ids map to the same target_id 0 \n",
"\tquery_ids map to multiple target_ids in the main mapper 0 \n",
"\tquery_ids map to multiple target_ids in the alternative mapper 31 \n",
"\tLOC not found in Entrez 115 \n",
"\tNot found at all: 6\n",
"Warning: query IDs mapping to duplicated target IDs in mapping table: 34\n",
"Warning: query IDs not mapped to any target IDs excluded: 152\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"IDs mapped to multiple target IDs are kept:\n",
" [143872, 84458, 51236, 119016, 6218, 653067, 286464, 79741, 644019, 284565, 374, 144535, 341019, 84316, 4253, 200030]\n"
]
},
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
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" vertical-align: middle;\n",
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"\n",
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" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Sample</th>\n",
" <th>Gene</th>\n",
" <th>Entrez</th>\n",
" <th>Category</th>\n",
" <th>Details</th>\n",
" <th>Entrez_gene_ID</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>X-1004</td>\n",
" <td>ABCA4</td>\n",
" <td>24</td>\n",
" <td>MutNovel</td>\n",
" <td>K1831N,0.550</td>\n",
" <td>24</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>X-1004</td>\n",
" <td>ADAM17</td>\n",
" <td>6868</td>\n",
" <td>MutNovel</td>\n",
" <td>P799T,1.000</td>\n",
" <td>6868</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>X-1004</td>\n",
" <td>ADCK1</td>\n",
" <td>57143</td>\n",
" <td>MutNovel</td>\n",
" <td>D52G,1.000</td>\n",
" <td>57143</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>X-1004</td>\n",
" <td>ADNP</td>\n",
" <td>23394</td>\n",
" <td>MutNovel</td>\n",
" <td>R784T,0.223</td>\n",
" <td>23394</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>X-1004</td>\n",
" <td>AK1</td>\n",
" <td>203</td>\n",
" <td>MutNovel</td>\n",
" <td>K27N,0.430</td>\n",
" <td>203</td>\n",
" </tr>\n",
" <tr>\n",
" <th>32</th>\n",
" <td>X-1004</td>\n",
" <td>AMOTL2</td>\n",
" <td>51421</td>\n",
" <td>MutNovel</td>\n",
" <td>A578P,0.625</td>\n",
" <td>51421</td>\n",
" </tr>\n",
" <tr>\n",
" <th>37</th>\n",
" <td>X-1004</td>\n",
" <td>ANKRD36</td>\n",
" <td>375248</td>\n",
" <td>MutNovel</td>\n",
" <td>T998S,0.278</td>\n",
" <td>375248</td>\n",
" </tr>\n",
" <tr>\n",
" <th>38</th>\n",
" <td>X-1004</td>\n",
" <td>ANKRD62</td>\n",
" <td>None</td>\n",
" <td>MutNovel</td>\n",
" <td>N547T,1.000</td>\n",
" <td>342850</td>\n",
" </tr>\n",
" <tr>\n",
" <th>41</th>\n",
" <td>X-1004</td>\n",
" <td>ANXA7</td>\n",
" <td>310</td>\n",
" <td>MutNovel</td>\n",
" <td>I283V,0.565</td>\n",
" <td>310</td>\n",
" </tr>\n",
" <tr>\n",
" <th>43</th>\n",
" <td>X-1004</td>\n",
" <td>APLF</td>\n",
" <td>200558</td>\n",
" <td>MutNovel</td>\n",
" <td>I237V,0.556</td>\n",
" <td>200558</td>\n",
" </tr>\n",
" <tr>\n",
" <th>48</th>\n",
" <td>X-1004</td>\n",
" <td>ARMC2</td>\n",
" <td>84071</td>\n",
" <td>MutNovel</td>\n",
" <td>E283G,1.000</td>\n",
" <td>84071</td>\n",
" </tr>\n",
" <tr>\n",
" <th>52</th>\n",
" <td>X-1004</td>\n",
" <td>ASTN1</td>\n",
" <td>460</td>\n",
" <td>MutNovel</td>\n",
" <td>S1091C,0.443</td>\n",
" <td>460</td>\n",
" </tr>\n",
" <tr>\n",
" <th>57</th>\n",
" <td>X-1004</td>\n",
" <td>ATRX</td>\n",
" <td>546</td>\n",
" <td>MutNovel</td>\n",
" <td>P711A,1.000</td>\n",
" <td>546</td>\n",
" </tr>\n",
" <tr>\n",
" <th>59</th>\n",
" <td>X-1004</td>\n",
" <td>AVIL</td>\n",
" <td>10677</td>\n",
" <td>MutNovel</td>\n",
" <td>A455T,1.000</td>\n",
" <td>10677</td>\n",
" </tr>\n",
" <tr>\n",
" <th>62</th>\n",
" <td>X-1004</td>\n",
" <td>BAG6</td>\n",
" <td>7917</td>\n",
" <td>MutNovel</td>\n",
" <td>L733I,0.547</td>\n",
" <td>7917</td>\n",
" </tr>\n",
" <tr>\n",
" <th>69</th>\n",
" <td>X-1004</td>\n",
" <td>BIRC6</td>\n",
" <td>57448</td>\n",
" <td>MutNovel</td>\n",
" <td>A1405V,0.688</td>\n",
" <td>57448</td>\n",
" </tr>\n",
" <tr>\n",
" <th>88</th>\n",
" <td>X-1004</td>\n",
" <td>C16orf79</td>\n",
" <td>283870</td>\n",
" <td>MutNovel</td>\n",
" <td>I82M,1.000</td>\n",
" <td>283870</td>\n",
" </tr>\n",
" <tr>\n",
" <th>92</th>\n",
" <td>X-1004</td>\n",
" <td>C1orf182</td>\n",
" <td>128229</td>\n",
" <td>MutNovel</td>\n",
" <td>A80T,1.000</td>\n",
" <td>128229</td>\n",
" </tr>\n",
" <tr>\n",
" <th>106</th>\n",
" <td>X-1004</td>\n",
" <td>CARM1</td>\n",
" <td>10498</td>\n",
" <td>MutNovel</td>\n",
" <td>K81N,0.280</td>\n",
" <td>10498</td>\n",
" </tr>\n",
" <tr>\n",
" <th>110</th>\n",
" <td>X-1004</td>\n",
" <td>CBWD1</td>\n",
" <td>55871</td>\n",
" <td>MutNovel</td>\n",
" <td>N363I,0.893</td>\n",
" <td>55871</td>\n",
" </tr>\n",
" <tr>\n",
" <th>115</th>\n",
" <td>X-1004</td>\n",
" <td>CCDC66</td>\n",
" <td>285331</td>\n",
" <td>MutNovel</td>\n",
" <td>R538P,1.000</td>\n",
" <td>285331</td>\n",
" </tr>\n",
" <tr>\n",
" <th>116</th>\n",
" <td>X-1004</td>\n",
" <td>CCDC88A</td>\n",
" <td>55704</td>\n",
" <td>MutNovel</td>\n",
" <td>E217A,0.263</td>\n",
" <td>55704</td>\n",
" </tr>\n",
" <tr>\n",
" <th>119</th>\n",
" <td>X-1004</td>\n",
" <td>CCT7</td>\n",
" <td>10574</td>\n",
" <td>MutNovel</td>\n",
" <td>A162T,0.384</td>\n",
" <td>10574</td>\n",
" </tr>\n",
" <tr>\n",
" <th>124</th>\n",
" <td>X-1004</td>\n",
" <td>CDC42EP1</td>\n",
" <td>11135</td>\n",
" <td>MutNovel</td>\n",
" <td>PAPAANPS253P,0.833</td>\n",
" <td>11135</td>\n",
" </tr>\n",
" <tr>\n",
" <th>126</th>\n",
" <td>X-1004</td>\n",
" <td>CDON</td>\n",
" <td>50937</td>\n",
" <td>MutNovel</td>\n",
" <td>S483R,1.000</td>\n",
" <td>50937</td>\n",
" </tr>\n",
" <tr>\n",
" <th>133</th>\n",
" <td>X-1004</td>\n",
" <td>CENPV</td>\n",
" <td>201161</td>\n",
" <td>MutNovel</td>\n",
" <td>P24S,0.700</td>\n",
" <td>201161</td>\n",
" </tr>\n",
" <tr>\n",
" <th>135</th>\n",
" <td>X-1004</td>\n",
" <td>CEP350</td>\n",
" <td>9857</td>\n",
" <td>MutNovel</td>\n",
" <td>R214M,0.286</td>\n",
" <td>9857</td>\n",
" </tr>\n",
" <tr>\n",
" <th>143</th>\n",
" <td>X-1004</td>\n",
" <td>CHORDC1</td>\n",
" <td>26973</td>\n",
" <td>MutNovel</td>\n",
" <td>P31L,0.672</td>\n",
" <td>26973</td>\n",
" </tr>\n",
" <tr>\n",
" <th>145</th>\n",
" <td>X-1004</td>\n",
" <td>CHRNB4</td>\n",
" <td>1143</td>\n",
" <td>MutNovel</td>\n",
" <td>G226D,1.000</td>\n",
" <td>1143</td>\n",
" </tr>\n",
" <tr>\n",
" <th>150</th>\n",
" <td>X-1004</td>\n",
" <td>CLUAP1</td>\n",
" <td>23059</td>\n",
" <td>MutNovel</td>\n",
" <td>P348S,1.000</td>\n",
" <td>23059</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>125656</th>\n",
" <td>X-1726</td>\n",
" <td>2014-03-02 00:00:00</td>\n",
" <td>54996</td>\n",
" <td>MutNovel</td>\n",
" <td>F151S,0.442</td>\n",
" <td>54996</td>\n",
" </tr>\n",
" <tr>\n",
" <th>141280</th>\n",
" <td>X-3029</td>\n",
" <td>2014-03-06 00:00:00</td>\n",
" <td>10299</td>\n",
" <td>MutNovel</td>\n",
" <td>D142N,0.288</td>\n",
" <td>10299</td>\n",
" </tr>\n",
" <tr>\n",
" <th>141455</th>\n",
" <td>X-3029</td>\n",
" <td>2014-09-01 00:00:00</td>\n",
" <td>1731</td>\n",
" <td>MutNovel</td>\n",
" <td>R251H,0.364</td>\n",
" <td>1731</td>\n",
" </tr>\n",
" <tr>\n",
" <th>146922</th>\n",
" <td>X-4819</td>\n",
" <td>2014-03-04 00:00:00</td>\n",
" <td>57574</td>\n",
" <td>MutNovel</td>\n",
" <td>P368T,0.583</td>\n",
" <td>57574</td>\n",
" </tr>\n",
" <tr>\n",
" <th>151460</th>\n",
" <td>X-2602</td>\n",
" <td>2014-09-09 00:00:00</td>\n",
" <td>10801</td>\n",
" <td>MutNovel</td>\n",
" <td>A245V,0.528</td>\n",
" <td>10801</td>\n",
" </tr>\n",
" <tr>\n",
" <th>176127</th>\n",
" <td>X-5643</td>\n",
" <td>2014-03-02 00:00:00</td>\n",
" <td>51257</td>\n",
" <td>MutNovel</td>\n",
" <td>P34L,0.397</td>\n",
" <td>51257</td>\n",
" </tr>\n",
" <tr>\n",
" <th>176128</th>\n",
" <td>X-5643</td>\n",
" <td>2014-03-06 00:00:00</td>\n",
" <td>10299</td>\n",
" <td>MutNovel</td>\n",
" <td>P902S,0.297</td>\n",
" <td>10299</td>\n",
" </tr>\n",
" <tr>\n",
" <th>180164</th>\n",
" <td>X-5696</td>\n",
" <td>2014-03-02 00:00:00</td>\n",
" <td>54996</td>\n",
" <td>MutNovel</td>\n",
" <td>D131N,0.261</td>\n",
" <td>54996</td>\n",
" </tr>\n",
" <tr>\n",
" <th>180165</th>\n",
" <td>X-5696</td>\n",
" <td>2014-03-01 00:00:00</td>\n",
" <td>55016</td>\n",
" <td>MutNovel</td>\n",
" <td>T244I,0.267</td>\n",
" <td>55016</td>\n",
" </tr>\n",
" <tr>\n",
" <th>180166</th>\n",
" <td>X-5696</td>\n",
" <td>2014-03-05 00:00:00</td>\n",
" <td>54708</td>\n",
" <td>MutNovel</td>\n",
" <td>G80D,0.394</td>\n",
" <td>54708</td>\n",
" </tr>\n",
" <tr>\n",
" <th>180167</th>\n",
" <td>X-5696</td>\n",
" <td>2014-03-05 00:00:00</td>\n",
" <td>54708</td>\n",
" <td>MutNovel</td>\n",
" <td>G242E,0.442</td>\n",
" <td>54708</td>\n",
" </tr>\n",
" <tr>\n",
" <th>180168</th>\n",
" <td>X-5696</td>\n",
" <td>2014-03-06 00:00:00</td>\n",
" <td>10299</td>\n",
" <td>MutNovel</td>\n",
" <td>V161M,1.000</td>\n",
" <td>10299</td>\n",
" </tr>\n",
" <tr>\n",
" <th>180169</th>\n",
" <td>X-5696</td>\n",
" <td>2014-03-06 00:00:00</td>\n",
" <td>10299</td>\n",
" <td>MutNovel</td>\n",
" <td>G352S,0.568</td>\n",
" <td>10299</td>\n",
" </tr>\n",
" <tr>\n",
" <th>180170</th>\n",
" <td>X-5696</td>\n",
" <td>2014-03-09 00:00:00</td>\n",
" <td>92979</td>\n",
" <td>MutNovel</td>\n",
" <td>G20C,0.304</td>\n",
" <td>92979</td>\n",
" </tr>\n",
" <tr>\n",
" <th>181635</th>\n",
" <td>X-5696</td>\n",
" <td>2014-09-01 00:00:00</td>\n",
" <td>1731</td>\n",
" <td>MutNovel</td>\n",
" <td>D342N,0.352</td>\n",
" <td>1731</td>\n",
" </tr>\n",
" <tr>\n",
" <th>181636</th>\n",
" <td>X-5696</td>\n",
" <td>2014-09-02 00:00:00</td>\n",
" <td>4735</td>\n",
" <td>MutNovel</td>\n",
" <td>R229K,0.324</td>\n",
" <td>4735</td>\n",
" </tr>\n",
" <tr>\n",
" <th>181637</th>\n",
" <td>X-5696</td>\n",
" <td>2014-09-02 00:00:00</td>\n",
" <td>4735</td>\n",
" <td>MutNovel</td>\n",
" <td>G307D,0.321</td>\n",
" <td>4735</td>\n",
" </tr>\n",
" <tr>\n",
" <th>186444</th>\n",
" <td>X-5959</td>\n",
" <td>2014-09-09 00:00:00</td>\n",
" <td>10801</td>\n",
" <td>MutNovel</td>\n",
" <td>P256L,0.799</td>\n",
" <td>10801</td>\n",
" </tr>\n",
" <tr>\n",
" <th>191753</th>\n",
" <td>X-2607</td>\n",
" <td>2014-09-11 00:00:00</td>\n",
" <td>55752</td>\n",
" <td>MutNovel</td>\n",
" <td>V102M,0.266</td>\n",
" <td>55752</td>\n",
" </tr>\n",
" <tr>\n",
" <th>191754</th>\n",
" <td>X-2607</td>\n",
" <td>2014-09-07 00:00:00</td>\n",
" <td>989</td>\n",
" <td>MutNovel</td>\n",
" <td>Q393H,0.451</td>\n",
" <td>989</td>\n",
" </tr>\n",
" <tr>\n",
" <th>203713</th>\n",
" <td>X-4412</td>\n",
" <td>2014-03-07 00:00:00</td>\n",
" <td>64844</td>\n",
" <td>MutNovel</td>\n",
" <td>E599K,0.467</td>\n",
" <td>64844</td>\n",
" </tr>\n",
" <tr>\n",
" <th>206247</th>\n",
" <td>X-4852</td>\n",
" <td>2014-03-09 00:00:00</td>\n",
" <td>92979</td>\n",
" <td>MutNovel</td>\n",
" <td>C134S,0.412</td>\n",
" <td>92979</td>\n",
" </tr>\n",
" <tr>\n",
" <th>209729</th>\n",
" <td>X-1199</td>\n",
" <td>2014-09-08 00:00:00</td>\n",
" <td>23176</td>\n",
" <td>MutNovel</td>\n",
" <td>P16S,0.542</td>\n",
" <td>23176</td>\n",
" </tr>\n",
" <tr>\n",
" <th>219117</th>\n",
" <td>X-2633</td>\n",
" <td>2014-03-10 00:00:00</td>\n",
" <td>162333</td>\n",
" <td>MutNovel</td>\n",
" <td>A117G,0.667</td>\n",
" <td>162333</td>\n",
" </tr>\n",
" <tr>\n",
" <th>226988</th>\n",
" <td>X-4377</td>\n",
" <td>2014-03-09 00:00:00</td>\n",
" <td>92979</td>\n",
" <td>MutNovel</td>\n",
" <td>T107I,1.000</td>\n",
" <td>92979</td>\n",
" </tr>\n",
" <tr>\n",
" <th>227316</th>\n",
" <td>X-4378</td>\n",
" <td>2014-03-09 00:00:00</td>\n",
" <td>92979</td>\n",
" <td>MutNovel</td>\n",
" <td>T107I,0.400</td>\n",
" <td>92979</td>\n",
" </tr>\n",
" <tr>\n",
" <th>253499</th>\n",
" <td>X-4597</td>\n",
" <td>2014-09-07 00:00:00</td>\n",
" <td>989</td>\n",
" <td>MutNovel</td>\n",
" <td>L199F,0.484</td>\n",
" <td>989</td>\n",
" </tr>\n",
" <tr>\n",
" <th>257519</th>\n",
" <td>X-4979</td>\n",
" <td>2014-09-10 00:00:00</td>\n",
" <td>151011</td>\n",
" <td>MutNovel</td>\n",
" <td>R278C,0.524</td>\n",
" <td>151011</td>\n",
" </tr>\n",
" <tr>\n",
" <th>259068</th>\n",
" <td>X-5273</td>\n",
" <td>2014-09-08 00:00:00</td>\n",
" <td>23176</td>\n",
" <td>MutNovel</td>\n",
" <td>V384M,0.488</td>\n",
" <td>23176</td>\n",
" </tr>\n",
" <tr>\n",
" <th>259069</th>\n",
" <td>X-5273</td>\n",
" <td>2014-09-08 00:00:00</td>\n",
" <td>23176</td>\n",
" <td>MutNovel</td>\n",
" <td>P85F,0.564</td>\n",
" <td>23176</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>122412 rows × 6 columns</p>\n",
"</div>"
],
"text/plain": [
" Sample Gene Entrez Category Details \\\n",
"1 X-1004 ABCA4 24 MutNovel K1831N,0.550 \n",
"8 X-1004 ADAM17 6868 MutNovel P799T,1.000 \n",
"16 X-1004 ADCK1 57143 MutNovel D52G,1.000 \n",
"17 X-1004 ADNP 23394 MutNovel R784T,0.223 \n",
"21 X-1004 AK1 203 MutNovel K27N,0.430 \n",
"32 X-1004 AMOTL2 51421 MutNovel A578P,0.625 \n",
"37 X-1004 ANKRD36 375248 MutNovel T998S,0.278 \n",
"38 X-1004 ANKRD62 None MutNovel N547T,1.000 \n",
"41 X-1004 ANXA7 310 MutNovel I283V,0.565 \n",
"43 X-1004 APLF 200558 MutNovel I237V,0.556 \n",
"48 X-1004 ARMC2 84071 MutNovel E283G,1.000 \n",
"52 X-1004 ASTN1 460 MutNovel S1091C,0.443 \n",
"57 X-1004 ATRX 546 MutNovel P711A,1.000 \n",
"59 X-1004 AVIL 10677 MutNovel A455T,1.000 \n",
"62 X-1004 BAG6 7917 MutNovel L733I,0.547 \n",
"69 X-1004 BIRC6 57448 MutNovel A1405V,0.688 \n",
"88 X-1004 C16orf79 283870 MutNovel I82M,1.000 \n",
"92 X-1004 C1orf182 128229 MutNovel A80T,1.000 \n",
"106 X-1004 CARM1 10498 MutNovel K81N,0.280 \n",
"110 X-1004 CBWD1 55871 MutNovel N363I,0.893 \n",
"115 X-1004 CCDC66 285331 MutNovel R538P,1.000 \n",
"116 X-1004 CCDC88A 55704 MutNovel E217A,0.263 \n",
"119 X-1004 CCT7 10574 MutNovel A162T,0.384 \n",
"124 X-1004 CDC42EP1 11135 MutNovel PAPAANPS253P,0.833 \n",
"126 X-1004 CDON 50937 MutNovel S483R,1.000 \n",
"133 X-1004 CENPV 201161 MutNovel P24S,0.700 \n",
"135 X-1004 CEP350 9857 MutNovel R214M,0.286 \n",
"143 X-1004 CHORDC1 26973 MutNovel P31L,0.672 \n",
"145 X-1004 CHRNB4 1143 MutNovel G226D,1.000 \n",
"150 X-1004 CLUAP1 23059 MutNovel P348S,1.000 \n",
"... ... ... ... ... ... \n",
"125656 X-1726 2014-03-02 00:00:00 54996 MutNovel F151S,0.442 \n",
"141280 X-3029 2014-03-06 00:00:00 10299 MutNovel D142N,0.288 \n",
"141455 X-3029 2014-09-01 00:00:00 1731 MutNovel R251H,0.364 \n",
"146922 X-4819 2014-03-04 00:00:00 57574 MutNovel P368T,0.583 \n",
"151460 X-2602 2014-09-09 00:00:00 10801 MutNovel A245V,0.528 \n",
"176127 X-5643 2014-03-02 00:00:00 51257 MutNovel P34L,0.397 \n",
"176128 X-5643 2014-03-06 00:00:00 10299 MutNovel P902S,0.297 \n",
"180164 X-5696 2014-03-02 00:00:00 54996 MutNovel D131N,0.261 \n",
"180165 X-5696 2014-03-01 00:00:00 55016 MutNovel T244I,0.267 \n",
"180166 X-5696 2014-03-05 00:00:00 54708 MutNovel G80D,0.394 \n",
"180167 X-5696 2014-03-05 00:00:00 54708 MutNovel G242E,0.442 \n",
"180168 X-5696 2014-03-06 00:00:00 10299 MutNovel V161M,1.000 \n",
"180169 X-5696 2014-03-06 00:00:00 10299 MutNovel G352S,0.568 \n",
"180170 X-5696 2014-03-09 00:00:00 92979 MutNovel G20C,0.304 \n",
"181635 X-5696 2014-09-01 00:00:00 1731 MutNovel D342N,0.352 \n",
"181636 X-5696 2014-09-02 00:00:00 4735 MutNovel R229K,0.324 \n",
"181637 X-5696 2014-09-02 00:00:00 4735 MutNovel G307D,0.321 \n",
"186444 X-5959 2014-09-09 00:00:00 10801 MutNovel P256L,0.799 \n",
"191753 X-2607 2014-09-11 00:00:00 55752 MutNovel V102M,0.266 \n",
"191754 X-2607 2014-09-07 00:00:00 989 MutNovel Q393H,0.451 \n",
"203713 X-4412 2014-03-07 00:00:00 64844 MutNovel E599K,0.467 \n",
"206247 X-4852 2014-03-09 00:00:00 92979 MutNovel C134S,0.412 \n",
"209729 X-1199 2014-09-08 00:00:00 23176 MutNovel P16S,0.542 \n",
"219117 X-2633 2014-03-10 00:00:00 162333 MutNovel A117G,0.667 \n",
"226988 X-4377 2014-03-09 00:00:00 92979 MutNovel T107I,1.000 \n",
"227316 X-4378 2014-03-09 00:00:00 92979 MutNovel T107I,0.400 \n",
"253499 X-4597 2014-09-07 00:00:00 989 MutNovel L199F,0.484 \n",
"257519 X-4979 2014-09-10 00:00:00 151011 MutNovel R278C,0.524 \n",
"259068 X-5273 2014-09-08 00:00:00 23176 MutNovel V384M,0.488 \n",
"259069 X-5273 2014-09-08 00:00:00 23176 MutNovel P85F,0.564 \n",
"\n",
" Entrez_gene_ID \n",
"1 24 \n",
"8 6868 \n",
"16 57143 \n",
"17 23394 \n",
"21 203 \n",
"32 51421 \n",
"37 375248 \n",
"38 342850 \n",
"41 310 \n",
"43 200558 \n",
"48 84071 \n",
"52 460 \n",
"57 546 \n",
"59 10677 \n",
"62 7917 \n",
"69 57448 \n",
"88 283870 \n",
"92 128229 \n",
"106 10498 \n",
"110 55871 \n",
"115 285331 \n",
"116 55704 \n",
"119 10574 \n",
"124 11135 \n",
"126 50937 \n",
"133 201161 \n",
"135 9857 \n",
"143 26973 \n",
"145 1143 \n",
"150 23059 \n",
"... ... \n",
"125656 54996 \n",
"141280 10299 \n",
"141455 1731 \n",
"146922 57574 \n",
"151460 10801 \n",
"176127 51257 \n",
"176128 10299 \n",
"180164 54996 \n",
"180165 55016 \n",
"180166 54708 \n",
"180167 54708 \n",
"180168 10299 \n",
"180169 10299 \n",
"180170 92979 \n",
"181635 1731 \n",
"181636 4735 \n",
"181637 4735 \n",
"186444 10801 \n",
"191753 55752 \n",
"191754 989 \n",
"203713 64844 \n",
"206247 92979 \n",
"209729 23176 \n",
"219117 162333 \n",
"226988 92979 \n",
"227316 92979 \n",
"253499 989 \n",
"257519 151011 \n",
"259068 23176 \n",
"259069 23176 \n",
"\n",
"[122412 rows x 6 columns]"
]
},
"execution_count": 24,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# annotate genes \n",
"PDX_genes = pdx[[\"Gene\"]].copy()\n",
"PDX_genes.drop_duplicates(inplace = True)\n",
"print(\"mutated genes in PDX cohort\",PDX_genes.shape[0])\n",
"PDX_genes.set_index(\"Gene\",drop=False,inplace=True)\n",
"# rename with mapper \n",
"PDX_genes, query2target, not_mapped = apply_mappers(PDX_genes, ncbi_symbols, ncbi_synonyms, verbose = True,handle_duplicates = \"keep\")\n",
"pdx = pdx.loc[~pdx[\"Gene\"].isin(not_mapped),:]\n",
"pdx[\"Entrez_gene_ID\"] = pdx[\"Gene\"].apply(lambda x : query2target[x])\n",
"\n",
"# keep not mapped genes with Entrez IDs provided\n",
"pdx_not_mapped = pdx.loc[pdx[\"Gene\"].isin(not_mapped),:]\n",
"pdx_not_mapped = pdx_not_mapped.loc[pdx_not_mapped[\"Entrez\"]!=\"None\",:]\n",
"pdx_not_mapped[\"Entrez_gene_ID\"] = pdx_not_mapped[\"Entrez\"].apply(int)\n",
"\n",
"# concatenate \n",
"pdx = pd.concat([pdx,pdx_,pdx_not_mapped],axis=0)\n",
"pdx "
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
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"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Sample</th>\n",
" <th>Entrez_gene_ID</th>\n",
" <th>Details</th>\n",
" <th>Gene</th>\n",
" <th>Category</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>X-1004</td>\n",
" <td>24</td>\n",
" <td>K1831N,0.550</td>\n",
" <td>ABCA4</td>\n",
" <td>MutNovel</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>X-1004</td>\n",
" <td>203</td>\n",
" <td>K27N,0.430</td>\n",
" <td>AK1</td>\n",
" <td>MutNovel</td>\n",
" </tr>\n",
" <tr>\n",
" <th>41</th>\n",
" <td>X-1004</td>\n",
" <td>310</td>\n",
" <td>I283V,0.565</td>\n",
" <td>ANXA7</td>\n",
" <td>MutNovel</td>\n",
" </tr>\n",
" <tr>\n",
" <th>52</th>\n",
" <td>X-1004</td>\n",
" <td>460</td>\n",
" <td>S1091C,0.443</td>\n",
" <td>ASTN1</td>\n",
" <td>MutNovel</td>\n",
" </tr>\n",
" <tr>\n",
" <th>57</th>\n",
" <td>X-1004</td>\n",
" <td>546</td>\n",
" <td>P711A,1.000</td>\n",
" <td>ATRX</td>\n",
" <td>MutNovel</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" Sample Entrez_gene_ID Details Gene Category\n",
"1 X-1004 24 K1831N,0.550 ABCA4 MutNovel\n",
"21 X-1004 203 K27N,0.430 AK1 MutNovel\n",
"41 X-1004 310 I283V,0.565 ANXA7 MutNovel\n",
"52 X-1004 460 S1091C,0.443 ASTN1 MutNovel\n",
"57 X-1004 546 P711A,1.000 ATRX MutNovel"
]
},
"execution_count": 25,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# define positions and mutation types\n",
"pdx = pdx.sort_values([\"Sample\",\"Entrez_gene_ID\"])\n",
"pdx = pdx.loc[:,[\"Sample\",\"Entrez_gene_ID\",\"Details\",\"Gene\",\"Category\"]]\n",
"pdx.head(5)"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {},
"outputs": [],
"source": [
"#pdx.loc[pdx[\"Details\"].str.contains(\"\\-\"),:].sort_values(\"Sample\").shape\n",
"#pdx.loc[pdx[\"Gene\"] == \"TTN\",:].sort_values(\"Sample\")\n",
"#pdx.loc[pdx[\"Category\"]==\"MutLikelyFunctional\",:].sort_values(\"Sample\")"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Classification\n",
"missense 99349\n",
"inframe_indel 8559\n",
"unrecognized_truncating 4624\n",
"stop_gain_or_fs 3788\n",
"unrecognized_point2 2245\n",
"ess_splice 2204\n",
"unrecognized_point 1643\n",
"dtype: int64"
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# guess mutation type from \"Details\" field\n",
"def guess_mut_type(x):\n",
" mut = x.split(\",\")[0]\n",
" missense_pattern = re.compile(\"^[A-Z][0-9]+[A-Z]$\")\n",
" indel_pattern = re.compile(\"^[A-Z]+[0-9]+[A-Z]+$\")\n",
" #stop_gain_pattern = re.compile(\"^[A-Z][0-9]+\\*$\")\n",
" if bool(re.match(missense_pattern ,mut)): # missense\n",
" return \"missense\"\n",
" elif bool(re.match(indel_pattern ,mut)): # indel inframe\n",
" return \"inframe_indel\"\n",
" elif \"*\" in mut: #bool(re.match(stop_gain_pattern,mut)): \n",
" return \"stop_gain_or_fs\" #print(mut)\n",
" elif \"?\" in mut: # splice_site\n",
" return \"ess_splice\" #print(mut)\n",
" elif bool(re.match(re.compile(\"^\\-[0-9]+[A-Z]+$\"),mut)): # -64Q - always MutNovel\n",
" return \"unrecognized_point\"\n",
" elif bool(re.match(re.compile(\"^\\-[0-9]+$\"),mut)): # -509 mostly MutKnownFunctional\n",
" return \"unrecognized_truncating\"\n",
" elif bool(re.match(re.compile(\"^[A-Z]+[0-9]+\\-$\"),mut)): #Q72- mutNovel\n",
" return \"unrecognized_point2\"\n",
" else:\n",
" return \"unrecognized\"\n",
"#for d in pdx[\"Details\"].values:\n",
" \n",
"pdx[\"Classification\"] = pdx[\"Details\"].apply(guess_mut_type)\n",
"#pdx.loc[pdx[\"Classification\"].str.contains(\"unrecognized\"),:].groupby([\"Category\",\"Classification\"]).size()\n",
"pdx.groupby([\"Classification\"]).size().sort_values(ascending = False)\n",
"#pdx.loc[pdx[\"Classification\"]==\"unrecognized\",:]"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"function\n",
"point_mutation 111796\n",
"truncating_mutation 10616\n",
"dtype: int64"
]
},
"execution_count": 28,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pdx_truncating = ['stop_gain_or_fs','ess_splice',\"unrecognized_truncating\"]\n",
"pdx_point = ['missense','inframe_indel','unrecognized_point','unrecognized_point2']\n",
"pdx.loc[pdx[\"Classification\"].isin(pdx_truncating),\"function\"] = \"truncating_mutation\"\n",
"pdx.loc[pdx[\"Classification\"].isin(pdx_point),\"function\"] = \"point_mutation\"\n",
"pdx.groupby([\"function\"]).size().sort_values(ascending = False)"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Sample</th>\n",
" <th>Entrez_gene_ID</th>\n",
" <th>Details</th>\n",
" <th>Gene</th>\n",
" <th>Category</th>\n",
" <th>Classification</th>\n",
" <th>function</th>\n",
" <th>aa_change</th>\n",
" <th>aa_pos</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>X-1004</td>\n",
" <td>24</td>\n",
" <td>K1831N,0.550</td>\n",
" <td>ABCA4</td>\n",
" <td>MutNovel</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>K1831N</td>\n",
" <td>(1831, 1831)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>X-1004</td>\n",
" <td>203</td>\n",
" <td>K27N,0.430</td>\n",
" <td>AK1</td>\n",
" <td>MutNovel</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>K27N</td>\n",
" <td>(27, 27)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>41</th>\n",
" <td>X-1004</td>\n",
" <td>310</td>\n",
" <td>I283V,0.565</td>\n",
" <td>ANXA7</td>\n",
" <td>MutNovel</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>I283V</td>\n",
" <td>(283, 283)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>52</th>\n",
" <td>X-1004</td>\n",
" <td>460</td>\n",
" <td>S1091C,0.443</td>\n",
" <td>ASTN1</td>\n",
" <td>MutNovel</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>S1091C</td>\n",
" <td>(1091, 1091)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>57</th>\n",
" <td>X-1004</td>\n",
" <td>546</td>\n",
" <td>P711A,1.000</td>\n",
" <td>ATRX</td>\n",
" <td>MutNovel</td>\n",
" <td>missense</td>\n",
" <td>point_mutation</td>\n",
" <td>P711A</td>\n",
" <td>(711, 711)</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" Sample Entrez_gene_ID Details Gene Category Classification \\\n",
"1 X-1004 24 K1831N,0.550 ABCA4 MutNovel missense \n",
"21 X-1004 203 K27N,0.430 AK1 MutNovel missense \n",
"41 X-1004 310 I283V,0.565 ANXA7 MutNovel missense \n",
"52 X-1004 460 S1091C,0.443 ASTN1 MutNovel missense \n",
"57 X-1004 546 P711A,1.000 ATRX MutNovel missense \n",
"\n",
" function aa_change aa_pos \n",
"1 point_mutation K1831N (1831, 1831) \n",
"21 point_mutation K27N (27, 27) \n",
"41 point_mutation I283V (283, 283) \n",
"52 point_mutation S1091C (1091, 1091) \n",
"57 point_mutation P711A (711, 711) "
]
},
"execution_count": 29,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pdx[\"aa_change\"] = pdx[\"Details\"].apply(lambda x: x.split(\",\")[0])\n",
"pdx[\"aa_pos\"] = pdx[\"aa_change\"].apply(lambda x : get_aa_pos_GDSC(x))\n",
"pdx.head()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {},
"outputs": [
{
"data": {
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>X-1004</th>\n",
" <th>X-1008</th>\n",
" <th>X-1027</th>\n",
" <th>X-1095</th>\n",
" <th>X-1119</th>\n",
" <th>X-1156</th>\n",
" <th>X-1167</th>\n",
" <th>X-1169</th>\n",
" <th>X-1172</th>\n",
" <th>X-1173</th>\n",
" <th>...</th>\n",
" <th>X-5713</th>\n",
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" <th>X-5727</th>\n",
" <th>X-5739</th>\n",
" <th>X-5808</th>\n",
" <th>X-5959</th>\n",
" <th>X-5974</th>\n",
" <th>X-5975</th>\n",
" <th>X-6030</th>\n",
" <th>X-6047</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>7157</th>\n",
" <td>-1.0</td>\n",
" <td>-1.00</td>\n",
" <td>-1.0</td>\n",
" <td>0.0</td>\n",
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" <td>0.0</td>\n",
" <td>...</td>\n",
" <td>0.0</td>\n",
" <td>-1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>-1.000000</td>\n",
" <td>0.0</td>\n",
" <td>-1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>-1.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5290</th>\n",
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" <td>0.055556</td>\n",
" <td>0.0</td>\n",
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" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2312</th>\n",
" <td>0.0</td>\n",
" <td>-0.05</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
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" <td>0.0</td>\n",
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" <td>0.0</td>\n",
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" <tr>\n",
" <th>4893</th>\n",
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"</div>"
],
"text/plain": [
" X-1004 X-1008 X-1027 X-1095 X-1119 X-1156 X-1167 X-1169 X-1172 \\\n",
"7157 -1.0 -1.00 -1.0 0.0 0.0 -1.0 -0.5 -1.0 -1.00 \n",
"5290 0.0 0.00 0.0 0.0 0.0 0.0 0.0 0.0 0.00 \n",
"3845 0.0 0.00 1.0 1.0 0.0 1.0 0.0 0.0 1.00 \n",
"2312 0.0 -0.05 0.0 0.0 0.0 0.0 0.0 0.0 -0.05 \n",
"4893 0.0 0.00 0.0 0.0 0.0 0.0 0.0 0.0 0.00 \n",
"\n",
" X-1173 ... X-5713 X-5717 X-5727 X-5739 X-5808 X-5959 \\\n",
"7157 0.0 ... 0.0 -1.0 0.0 0.0 -1.000000 0.0 \n",
"5290 0.0 ... 0.0 0.0 0.0 0.0 0.055556 0.0 \n",
"3845 1.0 ... 0.0 1.0 0.0 0.0 1.000000 0.0 \n",
"2312 0.0 ... 0.0 0.0 0.0 0.0 0.000000 0.0 \n",
"4893 -1.0 ... 0.0 0.0 -1.0 0.0 0.000000 0.0 \n",
"\n",
" X-5974 X-5975 X-6030 X-6047 \n",
"7157 -1.0 0.0 0.0 -1.0 \n",
"5290 0.0 0.0 0.0 0.0 \n",
"3845 0.0 0.0 1.0 0.0 \n",
"2312 0.0 0.0 0.0 0.0 \n",
"4893 0.0 0.0 0.0 0.0 \n",
"\n",
"[5 rows x 399 columns]"
]
},
"execution_count": 30,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# calculate per gene scores: \n",
"pdx_scores = {}\n",
"for sample in list(set(pdx[\"Sample\"].values)):\n",
" df = pdx.loc[pdx[\"Sample\"] == sample,:]\n",
" pdx_scores[sample] = mutations2score(df, TSG_entrez,OG_entrez, hotspots, w=w)\n",
"pdx_scores = pd.DataFrame.from_dict(pdx_scores)\n",
"pdx_scores.fillna(0,inplace=True)\n",
"\n",
"pdx_scores.to_csv(preprocessed_dir+\"/PDX.non_bin_mutations.tsv\",sep = \"\\t\")\n",
"pdx_scores.loc[[7157,5290,3845,2312,4893],:]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {},
"outputs": [
{
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" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
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" <tr>\n",
" <th>4893</th>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
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" <td>0.0</td>\n",
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" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>...</td>\n",
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" </tbody>\n",
"</table>\n",
"<p>5 rows × 399 columns</p>\n",
"</div>"
],
"text/plain": [
" X-1004 X-1008 X-1027 X-1095 X-1119 X-1156 X-1167 X-1169 X-1172 \\\n",
"7157 1.0 1.0 1.0 0.0 0.0 1.0 1.0 1.0 1.0 \n",
"5290 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 \n",
"3845 0.0 0.0 1.0 1.0 0.0 1.0 0.0 0.0 1.0 \n",
"2312 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 \n",
"4893 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 \n",
"\n",
" X-1173 ... X-5713 X-5717 X-5727 X-5739 X-5808 X-5959 X-5974 \\\n",
"7157 0.0 ... 0.0 1.0 0.0 0.0 1.0 0.0 1.0 \n",
"5290 0.0 ... 0.0 0.0 0.0 0.0 1.0 0.0 0.0 \n",
"3845 1.0 ... 0.0 1.0 0.0 0.0 1.0 0.0 0.0 \n",
"2312 0.0 ... 0.0 0.0 0.0 0.0 0.0 0.0 0.0 \n",
"4893 1.0 ... 0.0 0.0 1.0 0.0 0.0 0.0 0.0 \n",
"\n",
" X-5975 X-6030 X-6047 \n",
"7157 0.0 0.0 1.0 \n",
"5290 0.0 0.0 0.0 \n",
"3845 0.0 1.0 0.0 \n",
"2312 0.0 0.0 0.0 \n",
"4893 0.0 0.0 0.0 \n",
"\n",
"[5 rows x 399 columns]"
]
},
"execution_count": 31,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pdx_scores = pdx_scores.applymap(lambda x: binarize(x))\n",
"pdx_scores.to_csv(preprocessed_dir+\"/PDX.binary_mutations.tsv\",sep = \"\\t\")\n",
"pdx_scores.loc[[7157,5290,3845,2312,4893],:]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# TCGA and CCLE \n",
" * in CCLE only 1651 genes were profiled. We used the file \"CCLE_hybrid_capture1650_hg19_NoCommonSNPs_CDS_2012.05.07.maf.gz\" marked as recommended. It contains a list of mutations across CCLE cell lines, with VAF > 10%, and common SNP excluded. \n",
" wget https://data.broadinstitute.org/ccle_legacy_data/hybrid_capture_sequencing/CCLE_hybrid_capture1650_hg19_NoCommonSNPs_CDS_2012.05.07.maf.gz\n",
" \n",
" Other source files:\n",
" * \"List of mutations in 1651 genes, determined by targeted massively parallel sequencing combined with Raindance technology\":\n",
" wget https://data.broadinstitute.org/ccle_legacy_data/hybrid_capture_sequencing/1650_HC_plus_RD_muts.maf.annotated\n",
" wget https://data.broadinstitute.org/ccle_legacy_data/hybrid_capture_sequencing/1650_HC_plus_RD_indels.maf.annotated\n",
" \n",
" \n",
" Union contains 120 OG and 182 TSG"
]
},
{
"cell_type": "code",
"execution_count": 177,
"metadata": {},
"outputs": [],
"source": [
"def read_broad_maf(df, point, truncating, protein_change = \"Protein_Change\"):\n",
" df = df[[\"Hugo_Symbol\",\"Entrez_Gene_Id\",\"Variant_Classification\",\n",
" protein_change,'Tumor_Sample_Barcode']].copy()\n",
" # 'Chromosome', u'Start_position', u'End_position']].copy()\n",
" if \"-Tumor\" in df[\"Tumor_Sample_Barcode\"].values[0]:\n",
" df[\"Tumor_Sample_Barcode\"] = df[\"Tumor_Sample_Barcode\"].apply(lambda x : x.replace(\"-Tumor\",\"\") )\n",
" df.sort_values([\"Tumor_Sample_Barcode\",\"Hugo_Symbol\"], inplace=True)\n",
" df = df.loc[~df[\"Variant_Classification\"].isin([\"3'UTR\",\"5'Flank\",\"5'UTR\",\"Intron\",\"Silent\",\"RNA\",\n",
" \"De_novo_Start_OutOfFrame\",'De_novo_Start_InFrame']),:]\n",
" \n",
" if df.shape[0] == 0:\n",
" return df.rename({\"Entrez_Gene_Id\":\"Entrez_gene_ID\",\"Tumor_Sample_Barcode\":\"Sample\"},axis =\"columns\")\n",
" df.loc[df[\"Variant_Classification\"].isin(truncating),\"function\"] = \"truncating_mutation\"\n",
" df.loc[df[\"Variant_Classification\"].isin(point),\"function\"] = \"point_mutation\"\n",
" df.loc[df[\"Variant_Classification\"].isin(['Splice_Site_DNP','Splice_Site_Ins','Splice_Site_SNP',\n",
" 'Start_Codon_Del','Stop_Codon_DNP','Stop_Codon_Ins']),\"Protein_Change\"] = \"NA\"\n",
" \n",
" df[\"aa_pos\"] = df[protein_change].apply(lambda x : get_aa_pos_GDSC(x))\n",
" df.rename({\"Entrez_Gene_Id\":\"Entrez_gene_ID\",\"Tumor_Sample_Barcode\":\"Sample\"},axis =\"columns\",inplace=True)\n",
" return df"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (4) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>Hugo_Symbol</th>\n",
" <th>Entrez_gene_ID</th>\n",
" <th>Variant_Classification</th>\n",
" <th>Protein_Change</th>\n",
" <th>Sample</th>\n",
" <th>function</th>\n",
" <th>aa_pos</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>76694</th>\n",
" <td>AAK1</td>\n",
" <td>22848</td>\n",
" <td>Missense_Mutation</td>\n",
" <td>p.R634H</td>\n",
" <td>22RV1_PROSTATE</td>\n",
" <td>point_mutation</td>\n",
" <td>(634, 634)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>37856</th>\n",
" <td>ABCC4</td>\n",
" <td>10257</td>\n",
" <td>Frame_Shift_Del</td>\n",
" <td>p.L883fs</td>\n",
" <td>22RV1_PROSTATE</td>\n",
" <td>truncating_mutation</td>\n",
" <td>(883, 883)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27083</th>\n",
" <td>ACACB</td>\n",
" <td>32</td>\n",
" <td>Missense_Mutation</td>\n",
" <td>p.R2360H</td>\n",
" <td>22RV1_PROSTATE</td>\n",
" <td>point_mutation</td>\n",
" <td>(2360, 2360)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>66125</th>\n",
" <td>ACVR2A</td>\n",
" <td>92</td>\n",
" <td>Frame_Shift_Del</td>\n",
" <td>p.K435fs</td>\n",
" <td>22RV1_PROSTATE</td>\n",
" <td>truncating_mutation</td>\n",
" <td>(435, 435)</td>\n",
" </tr>\n",
" <tr>\n",
" <th>46329</th>\n",
" <td>ADAMTSL3</td>\n",
" <td>57188</td>\n",
" <td>Missense_Mutation</td>\n",
" <td>p.G287D</td>\n",
" <td>22RV1_PROSTATE</td>\n",
" <td>point_mutation</td>\n",
" <td>(287, 287)</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" Hugo_Symbol Entrez_gene_ID Variant_Classification Protein_Change \\\n",
"76694 AAK1 22848 Missense_Mutation p.R634H \n",
"37856 ABCC4 10257 Frame_Shift_Del p.L883fs \n",
"27083 ACACB 32 Missense_Mutation p.R2360H \n",
"66125 ACVR2A 92 Frame_Shift_Del p.K435fs \n",
"46329 ADAMTSL3 57188 Missense_Mutation p.G287D \n",
"\n",
" Sample function aa_pos \n",
"76694 22RV1_PROSTATE point_mutation (634, 634) \n",
"37856 22RV1_PROSTATE truncating_mutation (883, 883) \n",
"27083 22RV1_PROSTATE point_mutation (2360, 2360) \n",
"66125 22RV1_PROSTATE truncating_mutation (435, 435) \n",
"46329 22RV1_PROSTATE point_mutation (287, 287) "
]
},
"execution_count": 32,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ccle_point = [\"Missense_Mutation\",\"In_Frame_Del\",\"In_Frame_Ins\"]\n",
"ccle_truncating = [\"Frame_Shift_Del\",\"Frame_Shift_Ins\",\"Nonsense_Mutation\",\n",
" \"Splice_Site_Ins\",\"Splice_Site_Del\",\"Splice_Site_SNP\",\"Splice_Site_DNP\",\n",
" \"Start_Codon_Del\",\"Stop_Codon_DNP\"]\n",
"\n",
"ccle = pd.read_csv(\"../../CCLE/CCLE_hybrid_capture1650_hg19_NoCommonSNPs_CDS_2012.05.07.maf\",sep=\"\\t\")\n",
"ccle = read_broad_maf(ccle, ccle_point, ccle_truncating)\n",
"ccle.head(5)"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"function\n",
"point_mutation 70503\n",
"truncating_mutation 18486\n",
"dtype: int64"
]
},
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ccle.groupby(\"Variant_Classification\").size().sort_values(ascending = False)\n",
"ccle.groupby(\"function\").size().sort_values(ascending = False)"
]
},
{
"cell_type": "code",
"execution_count": 34,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
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"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
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" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>22RV1_PROSTATE</th>\n",
" <th>2313287_STOMACH</th>\n",
" <th>253JBV_URINARY_TRACT</th>\n",
" <th>253J_URINARY_TRACT</th>\n",
" <th>42MGBA_CENTRAL_NERVOUS_SYSTEM</th>\n",
" <th>5637_URINARY_TRACT</th>\n",
" <th>59M_OVARY</th>\n",
" <th>639V_URINARY_TRACT</th>\n",
" <th>647V_URINARY_TRACT</th>\n",
" <th>697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE</th>\n",
" <th>...</th>\n",
" <th>WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE</th>\n",
" <th>YAPC_PANCREAS</th>\n",
" <th>YD10B_UPPER_AERODIGESTIVE_TRACT</th>\n",
" <th>YD15_SALIVARY_GLAND</th>\n",
" <th>YD38_UPPER_AERODIGESTIVE_TRACT</th>\n",
" <th>YD8_UPPER_AERODIGESTIVE_TRACT</th>\n",
" <th>YH13_CENTRAL_NERVOUS_SYSTEM</th>\n",
" <th>YKG1_CENTRAL_NERVOUS_SYSTEM</th>\n",
" <th>ZR751_BREAST</th>\n",
" <th>ZR7530_BREAST</th>\n",
" </tr>\n",
" </thead>\n",
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" <tr>\n",
" <th>7157</th>\n",
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" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" <td>0.0</td>\n",
" <td>...</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" <td>-1.0</td>\n",
" <td>-1.000000</td>\n",
" <td>0.000000</td>\n",
" <td>-1.0</td>\n",
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" <td>0.0</td>\n",
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" <th>5290</th>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
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" <td>0.0</td>\n",
" <td>0.5</td>\n",
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" <td>0.0</td>\n",
" <td>1.0</td>\n",
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" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.111111</td>\n",
" <td>0.000000</td>\n",
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" <td>0.0</td>\n",
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" <tr>\n",
" <th>4893</th>\n",
" <td>0.0</td>\n",
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"<p>4 rows × 905 columns</p>\n",
"</div>"
],
"text/plain": [
" 22RV1_PROSTATE 2313287_STOMACH 253JBV_URINARY_TRACT \\\n",
"7157 -1.0 0.0 0.0 \n",
"5290 1.0 0.0 1.0 \n",
"3845 0.0 0.0 0.0 \n",
"4893 0.0 0.0 0.0 \n",
"\n",
" 253J_URINARY_TRACT 42MGBA_CENTRAL_NERVOUS_SYSTEM 5637_URINARY_TRACT \\\n",
"7157 0.0 -1.0 -1.0 \n",
"5290 1.0 0.0 0.0 \n",
"3845 0.0 0.0 0.0 \n",
"4893 0.0 0.0 0.0 \n",
"\n",
" 59M_OVARY 639V_URINARY_TRACT 647V_URINARY_TRACT \\\n",
"7157 -1.0 -1.0 -1.0 \n",
"5290 0.0 0.5 0.0 \n",
"3845 0.0 1.0 0.0 \n",
"4893 0.0 -0.1 0.0 \n",
"\n",
" 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE ... \\\n",
"7157 0.0 ... \n",
"5290 0.0 ... \n",
"3845 0.0 ... \n",
"4893 -1.0 ... \n",
"\n",
" WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE YAPC_PANCREAS \\\n",
"7157 -1.0 -1.0 \n",
"5290 0.0 0.0 \n",
"3845 0.0 1.0 \n",
"4893 0.0 0.0 \n",
"\n",
" YD10B_UPPER_AERODIGESTIVE_TRACT YD15_SALIVARY_GLAND \\\n",
"7157 -1.0 -1.0 \n",
"5290 0.0 0.0 \n",
"3845 0.0 0.0 \n",
"4893 0.0 0.0 \n",
"\n",
" YD38_UPPER_AERODIGESTIVE_TRACT YD8_UPPER_AERODIGESTIVE_TRACT \\\n",
"7157 -1.0 -1.000000 \n",
"5290 0.0 0.000000 \n",
"3845 0.0 0.111111 \n",
"4893 0.0 0.000000 \n",
"\n",
" YH13_CENTRAL_NERVOUS_SYSTEM YKG1_CENTRAL_NERVOUS_SYSTEM ZR751_BREAST \\\n",
"7157 0.000000 -1.0 0.0 \n",
"5290 0.142857 1.0 0.0 \n",
"3845 0.000000 0.0 0.0 \n",
"4893 0.000000 0.0 0.0 \n",
"\n",
" ZR7530_BREAST \n",
"7157 0.0 \n",
"5290 0.0 \n",
"3845 0.0 \n",
"4893 0.0 \n",
"\n",
"[4 rows x 905 columns]"
]
},
"execution_count": 34,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ccle_scores = {}\n",
"for sample in list(set(ccle[\"Sample\"].values)):\n",
" df = ccle.loc[ccle[\"Sample\"] == sample,:]\n",
" ccle_scores[sample] = mutations2score(df, TSG_entrez,OG_entrez, hotspots, w=w)\n",
"ccle_scores = pd.DataFrame.from_dict(ccle_scores)\n",
"ccle_scores.fillna(0,inplace=True)\n",
"\n",
"ccle_scores.to_csv(preprocessed_dir+\"/CCLE.non_bin_mutations.tsv\",sep = \"\\t\")\n",
"ccle_scores.loc[[7157,5290,3845,4893],:]"
]
},
{
"cell_type": "code",
"execution_count": 35,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/home/olya/miniconda2/lib/python2.7/site-packages/pandas/core/indexing.py:1472: FutureWarning: \n",
"Passing list-likes to .loc or [] with any missing label will raise\n",
"KeyError in the future, you can use .reindex() as an alternative.\n",
"\n",
"See the documentation here:\n",
"https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike\n",
" return self._getitem_tuple(key)\n"
]
},
{
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" <th>647V_URINARY_TRACT</th>\n",
" <th>697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE</th>\n",
" <th>...</th>\n",
" <th>WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE</th>\n",
" <th>YAPC_PANCREAS</th>\n",
" <th>YD10B_UPPER_AERODIGESTIVE_TRACT</th>\n",
" <th>YD15_SALIVARY_GLAND</th>\n",
" <th>YD38_UPPER_AERODIGESTIVE_TRACT</th>\n",
" <th>YD8_UPPER_AERODIGESTIVE_TRACT</th>\n",
" <th>YH13_CENTRAL_NERVOUS_SYSTEM</th>\n",
" <th>YKG1_CENTRAL_NERVOUS_SYSTEM</th>\n",
" <th>ZR751_BREAST</th>\n",
" <th>ZR7530_BREAST</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>7157</th>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>...</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5290</th>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>...</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3845</th>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>...</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2312</th>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4893</th>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
" <td>...</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>5 rows × 905 columns</p>\n",
"</div>"
],
"text/plain": [
" 22RV1_PROSTATE 2313287_STOMACH 253JBV_URINARY_TRACT \\\n",
"7157 1.0 0.0 0.0 \n",
"5290 1.0 0.0 1.0 \n",
"3845 0.0 0.0 0.0 \n",
"2312 NaN NaN NaN \n",
"4893 0.0 0.0 0.0 \n",
"\n",
" 253J_URINARY_TRACT 42MGBA_CENTRAL_NERVOUS_SYSTEM 5637_URINARY_TRACT \\\n",
"7157 0.0 1.0 1.0 \n",
"5290 1.0 0.0 0.0 \n",
"3845 0.0 0.0 0.0 \n",
"2312 NaN NaN NaN \n",
"4893 0.0 0.0 0.0 \n",
"\n",
" 59M_OVARY 639V_URINARY_TRACT 647V_URINARY_TRACT \\\n",
"7157 1.0 1.0 1.0 \n",
"5290 0.0 1.0 0.0 \n",
"3845 0.0 1.0 0.0 \n",
"2312 NaN NaN NaN \n",
"4893 0.0 1.0 0.0 \n",
"\n",
" 697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE ... \\\n",
"7157 0.0 ... \n",
"5290 0.0 ... \n",
"3845 0.0 ... \n",
"2312 NaN ... \n",
"4893 1.0 ... \n",
"\n",
" WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE YAPC_PANCREAS \\\n",
"7157 1.0 1.0 \n",
"5290 0.0 0.0 \n",
"3845 0.0 1.0 \n",
"2312 NaN NaN \n",
"4893 0.0 0.0 \n",
"\n",
" YD10B_UPPER_AERODIGESTIVE_TRACT YD15_SALIVARY_GLAND \\\n",
"7157 1.0 1.0 \n",
"5290 0.0 0.0 \n",
"3845 0.0 0.0 \n",
"2312 NaN NaN \n",
"4893 0.0 0.0 \n",
"\n",
" YD38_UPPER_AERODIGESTIVE_TRACT YD8_UPPER_AERODIGESTIVE_TRACT \\\n",
"7157 1.0 1.0 \n",
"5290 0.0 0.0 \n",
"3845 0.0 1.0 \n",
"2312 NaN NaN \n",
"4893 0.0 0.0 \n",
"\n",
" YH13_CENTRAL_NERVOUS_SYSTEM YKG1_CENTRAL_NERVOUS_SYSTEM ZR751_BREAST \\\n",
"7157 0.0 1.0 0.0 \n",
"5290 1.0 1.0 0.0 \n",
"3845 0.0 0.0 0.0 \n",
"2312 NaN NaN NaN \n",
"4893 0.0 0.0 0.0 \n",
"\n",
" ZR7530_BREAST \n",
"7157 0.0 \n",
"5290 0.0 \n",
"3845 0.0 \n",
"2312 NaN \n",
"4893 0.0 \n",
"\n",
"[5 rows x 905 columns]"
]
},
"execution_count": 35,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ccle_scores = ccle_scores.applymap(lambda x: binarize(x))\n",
"ccle_scores.to_csv(preprocessed_dir+\"/CCLE.binary_mutations.tsv\",sep = \"\\t\")\n",
"ccle_scores.loc[[7157,5290,3845,2312,4893],:]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# TCGA\n",
"\n",
"### detected problems:\n",
"* no protein change field in 'KIPAN', 'OV', 'GBMLGG','COADREAD','LGG','KICH','KIRC' cohorts\n",
"* no input files for MESO\n",
"* protein change may be in fields \"Protein_Change\",\"amino_acid_change_WU\",\"AAChange\",\"amino_acid_change\" \n",
"* some missense mutations have no protein change.\n",
"* not clear what is 'R' protein change; these mutations excluded\n",
"* in some cohorts e.g. BRCA, Entrez_Gene_Id is 0 for all genes. We remapped HGNC symbols to Entrez Gene Id.\n",
"We skip mutations with Ensembl gene ID appeared in the column \"Hugo_Symbol\".\n",
"\n",
"Cohorts and mutaions without protein change were excluded."
]
},
{
"cell_type": "code",
"execution_count": 138,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Ok: no empty rows detected\n",
"Ok: no duplicated pairs detected\n",
"Ok: All Symbol rows are not empty.\n",
"Ok: All Symbol are mapped to GeneID\n",
"16 Symbol mapped to multiple GeneID\n",
"Ok: All GeneID are unique\n",
"59266 Symbol can be mapped directly to GeneID\n",
"Ok: no empty rows detected\n",
"Ok: no duplicated pairs detected\n",
"Ok: All Synonyms rows are not empty.\n",
"Ok: All Synonyms are mapped to GeneID\n",
"3145 Synonyms mapped to multiple GeneID\n",
"49179 different Synonyms mapped to the same GeneID\n",
"10839 Synonyms can be mapped directly to GeneID\n"
]
}
],
"source": [
"# remapping Hugo symbols to Entreze gene ids if necessary \n",
"NCBI = pd.read_csv(root_dir+\"Homo_sapiens.gene_info\",sep = \"\\t\")\n",
"NCBI = NCBI[[\"#tax_id\",\"GeneID\",\"Symbol\",\"Synonyms\",\"type_of_gene\"]]\n",
"NCBI = NCBI.loc[NCBI[\"#tax_id\"] == 9606]\n",
"NCBI = NCBI.loc[NCBI[\"type_of_gene\"] != \"unknown\"]\n",
"ncbi_symbols = parse_mapping_table(NCBI, \"Symbol\",\"GeneID\")\n",
"ncbi_synonyms = expand(NCBI[[\"Synonyms\",\"GeneID\"]],column=\"Synonyms\",sep=\"|\") \n",
"ncbi_synonyms = parse_mapping_table(ncbi_synonyms, \"Synonyms\",\"GeneID\")\n",
"def hgnc2entrez_mapper(df,ncbi_symbols,ncbi_synonyms):\n",
" remapped_df = df[[\"Entrez_gene_ID\",\"Hugo_Symbol\"]].copy()\n",
" remapped_df.drop_duplicates(inplace = True)\n",
" remapped_df.set_index(\"Hugo_Symbol\",inplace=True)\n",
" remapped_df,query2target,not_mapped = apply_mappers(remapped_df, ncbi_symbols, ncbi_synonyms,\n",
" verbose = False,handle_duplicates = \"keep\")\n",
" if len(not_mapped) > 0 :\n",
" print(len(not_mapped),\"Hugo symbols not mapped to Entrez gene ID\",not_mapped, file = sys.stderr)\n",
" df = df.loc[~df[\"Hugo_Symbol\"].isin(not_mapped),:].copy()\n",
" df[\"Entrez_gene_ID\"] = df[\"Hugo_Symbol\"].apply(lambda x:query2target[x])\n",
" return df"
]
},
{
"cell_type": "code",
"execution_count": 172,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"['ACC', 'TGCT', 'PCPG', 'BRCA', 'CHOL', 'THYM', 'UCEC', 'SKCM', 'PRAD', 'LIHC', 'ESCA', 'CESC', 'THCA', 'DLBC', 'GBM', 'UCS', 'LAML', 'HNSC', 'PAAD', 'LUAD', 'UVM', 'SARC', 'LGG', 'STAD', 'READ', 'KICH', 'KIRP', 'LUSC', 'STES', 'COAD', 'BLCA']\n"
]
}
],
"source": [
"cohorts = []\n",
"for f in os.listdir(\"../../TCGA/mutations/data/\"):\n",
" if f.endswith(\"tar.gz\"):\n",
" fp = f.replace(\".tar.gz\",\"\")\n",
" cohort = fp.split(\".\")[2].replace(\"org_\",\"\")\n",
" if not cohort in [\"KIPAN\",\"OV\",'GBMLGG','COADREAD','KIRC']: # 'LGG','KICH'\n",
" cohorts.append(cohort)\n",
"print(cohorts)"
]
},
{
"cell_type": "code",
"execution_count": 183,
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"ACC\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 91 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort ACC\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_ACC.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"583 TINAG 27283 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"583 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"93 GPX1 2876 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"93 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"369 YTHDF3 253943 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"369 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"106 GPX1 2876 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"106 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"99 GPR111 222611 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"99 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"123 GPX1 2876 In_Frame_Del point_mutation \n",
"\n",
" AAChange aa_pos \n",
"123 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"78 GPX1 2876 In_Frame_Del point_mutation \n",
"\n",
" AAChange aa_pos \n",
"78 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"137 BAHCC1 57597 In_Frame_Del point_mutation \n",
"\n",
" AAChange aa_pos \n",
"137 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"96 MROH8 140699 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"96 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function AAChange \\\n",
"2 NBPF1 55672 Missense_Mutation point_mutation . \n",
"\n",
" aa_pos \n",
"2 (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"50 GPX1 2876 In_Frame_Del point_mutation \n",
"\n",
" AAChange aa_pos \n",
"50 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"52 DIO3 1735 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"52 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"47 THSD7B 80731 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"47 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"274 BAHCC1 57597 In_Frame_Del point_mutation \n",
"333 LTBP4 8425 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"274 . (NA, NA) \n",
"333 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"186 DNAH11 8701 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"186 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"78 DNAH11 8701 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"78 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"180 C6orf10 10665 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"180 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"907 INPP5D 3635 Missense_Mutation point_mutation \n",
"929 MROH8 140699 Missense_Mutation point_mutation \n",
"36 NBPF1 55672 Missense_Mutation point_mutation \n",
"202 PCDH15 65217 Missense_Mutation point_mutation \n",
"852 THSD7B 80731 Missense_Mutation point_mutation \n",
"1128 UGT2B10 7365 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"907 . (NA, NA) \n",
"929 . (NA, NA) \n",
"36 . (NA, NA) \n",
"202 . (NA, NA) \n",
"852 . (NA, NA) \n",
"1128 . (NA, NA) \n",
"TCGA-PK-A5HB-01A-11D-A29I-10 ACC 6 point mutations without a position 1176 remain\n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"171 GPX1 2876 In_Frame_Del point_mutation \n",
"\n",
" AAChange aa_pos \n",
"171 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"159 GTPBP6 8225 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"159 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"429 PRKDC 5591 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"429 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"81 GPX1 2876 In_Frame_Del point_mutation \n",
"\n",
" AAChange aa_pos \n",
"81 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"591 DNAH11 8701 Missense_Mutation point_mutation \n",
"64 DRGX 644168 Missense_Mutation point_mutation \n",
"475 GPX1 2876 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"591 . (NA, NA) \n",
"64 . (NA, NA) \n",
"475 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"130 KRBA1 84626 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"130 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"100 EPT1 85465 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"100 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"138 RYK 6259 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"138 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"67 GPX1 2876 In_Frame_Del point_mutation \n",
"\n",
" AAChange aa_pos \n",
"67 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"2001 DNAH11 8701 Missense_Mutation point_mutation \n",
"1058 OAZ1 4946 Missense_Mutation point_mutation \n",
"1472 RIBC2 26150 Missense_Mutation point_mutation \n",
"1228 THSD7B 80731 Missense_Mutation point_mutation \n",
"2160 YTHDF3 253943 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"2001 . (NA, NA) \n",
"1058 . (NA, NA) \n",
"1472 . (NA, NA) \n",
"1228 . (NA, NA) \n",
"2160 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"134 TAP2 6891 Missense_Mutation point_mutation \n",
"141 ZAN 7455 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"134 . (NA, NA) \n",
"141 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"20 MIR662 724032 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"20 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"26 SHANK2 22941 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"26 . (NA, NA) \n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"TGCT\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 156 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort TGCT\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_TGCT.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"107 BCYRN1 6872 Missense_Mutation point_mutation \n",
"31 NPRL3 8131 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"107 . (NA, NA) \n",
"31 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"62 TXNRD2 10587 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"62 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"47 FRG1B 284802 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"47 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"49 FRG1B 284802 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"49 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"2 . 284498 Missense_Mutation point_mutation \n",
"3 . 284498 Missense_Mutation point_mutation \n",
"5 . 284498 Missense_Mutation point_mutation \n",
"7 . 284498 Missense_Mutation point_mutation \n",
"42 . 388761 Missense_Mutation point_mutation \n",
"43 . 388761 Missense_Mutation point_mutation \n",
"48 . 653365 Missense_Mutation point_mutation \n",
"55 . 4586 Missense_Mutation point_mutation \n",
"57 . 340990 Missense_Mutation point_mutation \n",
"58 . 340990 Missense_Mutation point_mutation \n",
"77 . 283463 Missense_Mutation point_mutation \n",
"79 . 283463 Missense_Mutation point_mutation \n",
"89 . 144535 Missense_Mutation point_mutation \n",
"168 . 23666 Missense_Mutation point_mutation \n",
"175 . 85354 Missense_Mutation point_mutation \n",
"181 . 5273 Missense_Mutation point_mutation \n",
"208 . 10130 Missense_Mutation point_mutation \n",
"261 . 339766 Missense_Mutation point_mutation \n",
"265 . 388795 Missense_Mutation point_mutation \n",
"293 . 152110 Missense_Mutation point_mutation \n",
"356 . 9425 Missense_Mutation point_mutation \n",
"357 . 9425 Missense_Mutation point_mutation \n",
"358 . 9425 Missense_Mutation point_mutation \n",
"359 . 9425 Missense_Mutation point_mutation \n",
"365 . 729583 Missense_Mutation point_mutation \n",
"466 . 286423 Missense_Mutation point_mutation \n",
"192 CAPNS1 826 In_Frame_Del point_mutation \n",
"286 GAS2L1 10634 Missense_Mutation point_mutation \n",
"252 LOC100507443 1419 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"2 . (NA, NA) \n",
"3 . (NA, NA) \n",
"5 . (NA, NA) \n",
"7 . (NA, NA) \n",
"42 . (NA, NA) \n",
"43 . (NA, NA) \n",
"48 . (NA, NA) \n",
"55 . (NA, NA) \n",
"57 . (NA, NA) \n",
"58 . (NA, NA) \n",
"77 . (NA, NA) \n",
"79 . (NA, NA) \n",
"89 . (NA, NA) \n",
"168 . (NA, NA) \n",
"175 . (NA, NA) \n",
"181 . (NA, NA) \n",
"208 . (NA, NA) \n",
"261 . (NA, NA) \n",
"265 . (NA, NA) \n",
"293 . (NA, NA) \n",
"356 . (NA, NA) \n",
"357 . (NA, NA) \n",
"358 . (NA, NA) \n",
"359 . (NA, NA) \n",
"365 . (NA, NA) \n",
"466 . (NA, NA) \n",
"192 . (NA, NA) \n",
"286 . (NA, NA) \n",
"252 . (NA, NA) \n",
"TCGA-W4-A7U3-01A-12D-A435-10 TGCT 29 point mutations without a position 67 remain\n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"11 . 256815 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"11 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"51 FBXL12 54850 Missense_Mutation point_mutation \n",
"53 NFIX 4784 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"51 . (NA, NA) \n",
"53 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"74 BCYRN1 6872 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"74 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"63 . 375748 Missense_Mutation point_mutation \n",
"41 RRBP1 6238 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"63 . (NA, NA) \n",
"41 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"63 . 29801 Missense_Mutation point_mutation \n",
"13 GRM5 2915 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"63 . (NA, NA) \n",
"13 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"35 ARHGEF4 50649 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"35 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"76 MAP3K14 9020 Missense_Mutation point_mutation \n",
"72 SAT1 6303 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"76 . (NA, NA) \n",
"72 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"103 INPP5D 3635 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"103 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"60 LTBP4 8425 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"60 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function AAChange \\\n",
"7 NBPF10 100132406 Missense_Mutation point_mutation . \n",
"\n",
" aa_pos \n",
"7 (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"88 ATG9B 285973 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"88 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"69 CECR2 27443 Missense_Mutation point_mutation \n",
"95 KRBA1 84626 Missense_Mutation point_mutation \n",
"90 ULBP3 79465 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"69 . (NA, NA) \n",
"95 . (NA, NA) \n",
"90 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"60 . 339766 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"60 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"46 . 400986 Missense_Mutation point_mutation \n",
"50 FRG1B 284802 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"46 . (NA, NA) \n",
"50 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"114 KRBA1 84626 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"114 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"39 FRG1B 284802 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"39 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"72 . 378108 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"72 . (NA, NA) \n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"72 FOLR3 2352 Missense_Mutation point_mutation \n",
"48 RRBP1 6238 Missense_Mutation point_mutation \n",
"73 SEPHS2 22928 Missense_Mutation point_mutation \n",
"74 TSPAN10 83882 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"72 . (NA, NA) \n",
"48 . (NA, NA) \n",
"73 . (NA, NA) \n",
"74 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"84 ZNF274 10782 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"84 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"47 OLFM2 93145 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"47 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"23 . 283685 In_Frame_Ins point_mutation \n",
"\n",
" AAChange aa_pos \n",
"23 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function AAChange \\\n",
"6 . 728841 Missense_Mutation point_mutation . \n",
"\n",
" aa_pos \n",
"6 (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"104 LTBP4 8425 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"104 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"51 RYK 6259 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"51 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"52 . 388795 Missense_Mutation point_mutation \n",
"84 DNM1 1759 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"52 . (NA, NA) \n",
"84 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"58 NUDT10 170685 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"58 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"38 ADAMTS10 81794 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"38 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"56 LTBP4 8425 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"56 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"155 TXNRD1 7296 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"155 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"16 . 283685 Missense_Mutation point_mutation \n",
"41 THADA 63892 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"16 . (NA, NA) \n",
"41 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"23 BAHCC1 57597 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"23 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"84 ATG9B 285973 Missense_Mutation point_mutation \n",
"93 EPT1 85465 Missense_Mutation point_mutation \n",
"94 GPX1 2876 Missense_Mutation point_mutation \n",
"7 PFKFB3 5209 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"84 . (NA, NA) \n",
"93 . (NA, NA) \n",
"94 . (NA, NA) \n",
"7 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"55 MAPK8IP2 23542 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"55 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"25 . 283685 In_Frame_Del point_mutation \n",
"\n",
" AAChange aa_pos \n",
"25 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"51 FRG1B 284802 Missense_Mutation point_mutation \n",
"80 MAPK8IP2 23542 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"51 . (NA, NA) \n",
"80 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"66 RRBP1 6238 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"66 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"85 . 30816 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"85 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"74 BAHCC1 57597 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"74 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"46 . 400986 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"46 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"17 . 283685 Missense_Mutation point_mutation \n",
"0 MST1L 11223 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"17 . (NA, NA) \n",
"0 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"90 KRBA1 84626 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"90 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"35 . 283463 Missense_Mutation point_mutation \n",
"51 ANKLE1 126549 In_Frame_Del point_mutation \n",
"\n",
" AAChange aa_pos \n",
"35 . (NA, NA) \n",
"51 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"60 FAM131A 131408 Missense_Mutation point_mutation \n",
"85 TAP2 6891 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"60 . (NA, NA) \n",
"85 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"59 FRG1B 284802 Missense_Mutation point_mutation \n",
"0 NBPF1 55672 Missense_Mutation point_mutation \n",
"55 THSD7B 80731 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"59 . (NA, NA) \n",
"0 . (NA, NA) \n",
"55 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"14 NACA 4666 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"14 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"11 . 388761 Missense_Mutation point_mutation \n",
"60 . 200958 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"11 . (NA, NA) \n",
"60 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"86 CPNE9 151835 Missense_Mutation point_mutation \n",
"39 ENDOV 284131 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"86 . (NA, NA) \n",
"39 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"36 FRG1B 284802 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"36 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"39 FAM101B 359845 Missense_Mutation point_mutation \n",
"65 FRG1B 284802 Missense_Mutation point_mutation \n",
"30 PCSK6 5046 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"39 . (NA, NA) \n",
"65 . (NA, NA) \n",
"30 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"53 FRG1B 284802 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"53 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"44 . 400986 Missense_Mutation point_mutation \n",
"84 . 84443 In_Frame_Del point_mutation \n",
"\n",
" AAChange aa_pos \n",
"44 . (NA, NA) \n",
"84 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"1 FPGT-TNNI3K 100144878 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"1 . (NA, NA) \n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"8 . 100288142 Missense_Mutation point_mutation \n",
"43 . 440348 Missense_Mutation point_mutation \n",
"56 . 400986 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"8 . (NA, NA) \n",
"43 . (NA, NA) \n",
"56 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"46 EPT1 85465 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"46 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"83 FAM86B1 85002 Missense_Mutation point_mutation \n",
"17 NACA 4666 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"83 . (NA, NA) \n",
"17 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"14 PELI3 246330 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"14 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"65 DNAH11 8701 Missense_Mutation point_mutation \n",
"66 DNAH11 8701 Missense_Mutation point_mutation \n",
"14 TUBA1A 7846 In_Frame_Del point_mutation \n",
"\n",
" AAChange aa_pos \n",
"65 . (NA, NA) \n",
"66 . (NA, NA) \n",
"14 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function AAChange \\\n",
"1 AGTRAP 57085 Missense_Mutation point_mutation . \n",
"\n",
" aa_pos \n",
"1 (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"78 CYP21A2 1589 Missense_Mutation point_mutation \n",
"33 UBFD1 56061 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"78 . (NA, NA) \n",
"33 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"62 . 728441 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"62 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"37 . 400986 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"37 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"56 RRBP1 6238 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"56 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"42 ZNF525 170958 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"42 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"33 MAP2K3 5606 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"33 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"45 . 7617 Missense_Mutation point_mutation \n",
"52 PDE6D 64708 Missense_Mutation point_mutation \n",
"90 TXNRD2 10587 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"45 . (NA, NA) \n",
"52 . (NA, NA) \n",
"90 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"53 . 253143 Missense_Mutation point_mutation \n",
"54 . 253143 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"53 . (NA, NA) \n",
"54 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"38 FAM101B 359845 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"38 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"54 . 400986 Missense_Mutation point_mutation \n",
"36 FAM101B 359845 Missense_Mutation point_mutation \n",
"33 PSKH1 5681 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"54 . (NA, NA) \n",
"36 . (NA, NA) \n",
"33 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"65 RIBC2 26150 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"65 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"33 EPCAM 4072 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"33 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"57 . 400986 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"57 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"0 MACF1 23499 Missense_Mutation point_mutation \n",
"22 MRPS11 64963 Missense_Mutation point_mutation \n",
"62 UGT2B10 7365 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"0 . (NA, NA) \n",
"22 . (NA, NA) \n",
"62 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"56 . 140731 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"56 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"26 SKOR1 390598 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"26 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"24 . 283685 In_Frame_Ins point_mutation \n",
"\n",
" AAChange aa_pos \n",
"24 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"119 MAPK8IP2 23542 Missense_Mutation point_mutation \n",
"65 NEURL2 140825 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"119 . (NA, NA) \n",
"65 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"65 BAHCC1 57597 Missense_Mutation point_mutation \n",
"41 RRBP1 6238 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"65 . (NA, NA) \n",
"41 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"47 FRG1B 284802 Missense_Mutation point_mutation \n",
"48 FRG1B 284802 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"47 . (NA, NA) \n",
"48 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"25 C13orf35 400165 Missense_Mutation point_mutation \n",
"53 FRG1B 284802 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"25 . (NA, NA) \n",
"53 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"36 . 9425 Missense_Mutation point_mutation \n",
"28 GYPC 2995 Missense_Mutation point_mutation \n",
"13 NACA 4666 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"36 . (NA, NA) \n",
"28 . (NA, NA) \n",
"13 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function AAChange \\\n",
"0 C1orf170 84808 Missense_Mutation point_mutation . \n",
"\n",
" aa_pos \n",
"0 (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"66 . 347265 Missense_Mutation point_mutation \n",
"72 BAHCC1 57597 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"66 . (NA, NA) \n",
"72 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"94 FOXP3 50943 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"94 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"88 DNM1 1759 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"88 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"4 . 728841 Missense_Mutation point_mutation \n",
"24 DOCK9 23348 Missense_Mutation point_mutation \n",
"109 PRKDC 5591 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"4 . (NA, NA) \n",
"24 . (NA, NA) \n",
"109 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"24 . 283463 Missense_Mutation point_mutation \n",
"25 . 283463 Missense_Mutation point_mutation \n",
"29 . 144453 Missense_Mutation point_mutation \n",
"70 . 339766 Missense_Mutation point_mutation \n",
"101 . 6960 Missense_Mutation point_mutation \n",
"106 . 347265 Missense_Mutation point_mutation \n",
"122 . 286423 Missense_Mutation point_mutation \n",
"17 C10orf105 414152 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"24 . (NA, NA) \n",
"25 . (NA, NA) \n",
"29 . (NA, NA) \n",
"70 . (NA, NA) \n",
"101 . (NA, NA) \n",
"106 . (NA, NA) \n",
"122 . (NA, NA) \n",
"17 . (NA, NA) \n",
"TCGA-VF-A8AA-01A-11D-A435-10 TGCT 8 point mutations without a position 27 remain\n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"2 . 284498 Missense_Mutation point_mutation \n",
"3 . 284498 Missense_Mutation point_mutation \n",
"10 . 780789 Missense_Mutation point_mutation \n",
"52 . 283463 Missense_Mutation point_mutation \n",
"54 . 283463 Missense_Mutation point_mutation \n",
"55 . 283463 Missense_Mutation point_mutation \n",
"56 . 283463 Missense_Mutation point_mutation \n",
"58 . 283463 Missense_Mutation point_mutation \n",
"63 . 144453 Missense_Mutation point_mutation \n",
"129 . 1550 Missense_Mutation point_mutation \n",
"149 . 339766 Missense_Mutation point_mutation \n",
"160 . 373856 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"2 . (NA, NA) \n",
"3 . (NA, NA) \n",
"10 . (NA, NA) \n",
"52 . (NA, NA) \n",
"54 . (NA, NA) \n",
"55 . (NA, NA) \n",
"56 . (NA, NA) \n",
"58 . (NA, NA) \n",
"63 . (NA, NA) \n",
"129 . (NA, NA) \n",
"149 . (NA, NA) \n",
"160 . (NA, NA) \n",
"TCGA-VF-A8A9-01A-11D-A435-10 TGCT 12 point mutations without a position 43 remain\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"89 SEPHS2 22928 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"89 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"61 CHIT1 1118 Missense_Mutation point_mutation \n",
"519 PRKDC 5591 Missense_Mutation point_mutation \n",
"52 RABGAP1L 9910 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"61 . (NA, NA) \n",
"519 . (NA, NA) \n",
"52 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"17 C1R 715 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"17 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"3 . 343170 Missense_Mutation point_mutation \n",
"76 SIMC1 375484 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"3 . (NA, NA) \n",
"76 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function AAChange \\\n",
"9 . 646309 Missense_Mutation point_mutation . \n",
"\n",
" aa_pos \n",
"9 (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"33 . 440348 Missense_Mutation point_mutation \n",
"71 PRKDC 5591 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"33 . (NA, NA) \n",
"71 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"45 LMCD1 29995 Missense_Mutation point_mutation \n",
"73 NPRL3 8131 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"45 . (NA, NA) \n",
"73 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"0 . 339457 Missense_Mutation point_mutation \n",
"1 . 339457 Missense_Mutation point_mutation \n",
"2 . 284498 Missense_Mutation point_mutation \n",
"3 . 284498 Missense_Mutation point_mutation \n",
"6 . 284498 Missense_Mutation point_mutation \n",
"38 . 388761 Missense_Mutation point_mutation \n",
"39 . 388761 Missense_Mutation point_mutation \n",
"44 . 653365 Missense_Mutation point_mutation \n",
"45 . 653045 Missense_Mutation point_mutation \n",
"52 . 340990 Missense_Mutation point_mutation \n",
"53 . 340990 Missense_Mutation point_mutation \n",
"55 . 340990 Missense_Mutation point_mutation \n",
"68 . 283463 Missense_Mutation point_mutation \n",
"70 . 283463 Missense_Mutation point_mutation \n",
"71 . 283463 Missense_Mutation point_mutation \n",
"94 . 319089 Missense_Mutation point_mutation \n",
"126 . 400555 Missense_Mutation point_mutation \n",
"127 . 400555 Missense_Mutation point_mutation \n",
"149 . 10130 Missense_Mutation point_mutation \n",
"151 . 10130 Missense_Mutation point_mutation \n",
"234 . 200958 Missense_Mutation point_mutation \n",
"255 . 9425 Missense_Mutation point_mutation \n",
"262 . 729583 Missense_Mutation point_mutation \n",
"338 . 84443 In_Frame_Del point_mutation \n",
"340 . 286423 Missense_Mutation point_mutation \n",
"146 CAPNS1 826 In_Frame_Del point_mutation \n",
"186 FRG1B 284802 Missense_Mutation point_mutation \n",
"178 LOC100507443 1419 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"0 . (NA, NA) \n",
"1 . (NA, NA) \n",
"2 . (NA, NA) \n",
"3 . (NA, NA) \n",
"6 . (NA, NA) \n",
"38 . (NA, NA) \n",
"39 . (NA, NA) \n",
"44 . (NA, NA) \n",
"45 . (NA, NA) \n",
"52 . (NA, NA) \n",
"53 . (NA, NA) \n",
"55 . (NA, NA) \n",
"68 . (NA, NA) \n",
"70 . (NA, NA) \n",
"71 . (NA, NA) \n",
"94 . (NA, NA) \n",
"126 . (NA, NA) \n",
"127 . (NA, NA) \n",
"149 . (NA, NA) \n",
"151 . (NA, NA) \n",
"234 . (NA, NA) \n",
"255 . (NA, NA) \n",
"262 . (NA, NA) \n",
"338 . (NA, NA) \n",
"340 . (NA, NA) \n",
"146 . (NA, NA) \n",
"186 . (NA, NA) \n",
"178 . (NA, NA) \n",
"TCGA-W4-A7U2-01A-11D-A435-10 TGCT 28 point mutations without a position 39 remain\n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"64 BAHCC1 57597 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"64 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"74 MMGT1 93380 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"74 . (NA, NA) \n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"PCPG\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 185 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort PCPG\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_PCPG.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"BRCA\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 983 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort BRCA\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_BRCA.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['EFTUD1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['KIAA1804']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000254553']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CD97']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['C2orf47']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 10\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"10 Hugo symbols not mapped to Entrez gene ID ['AZI1', 'CSRP2BP', 'DBC1', 'TCEB3C', 'ENSG00000249624', 'MT-ATP6', 'MT-CO3', 'MT-CYB', 'MT-ND3', 'MT-ND4']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000173366']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['KIAA1045']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['FAM21A']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['FAM18B2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['DBC1', 'ENSG00000226232']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000226232']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000184909']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['C10orf2', 'MLL2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000214397']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000176593', 'FLJ22184']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['KIAA1045']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000173366']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MLL2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 9\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"9 Hugo symbols not mapped to Entrez gene ID ['ADC', 'AIM1', 'C15orf38', 'CCBP2', 'CD97', 'EFTUD1', 'MLL2', 'TCEB3CL', 'ENSG00000235434']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000184909']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['HEATR8']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MLL2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000267261']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['DBC1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ADC', 'ODZ3']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['MT-CYB', 'MT-ND1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000248710']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MLL2']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000235041']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['FAM21A']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CXXC11']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CD97']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['PPYR1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['FAM21A']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CYB']"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"1 Hugo symbols not mapped to Entrez gene ID ['APITD1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['AIM1', 'FLJ43860']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CD97']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['CCBP2', 'FLJ43860']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs mapping to duplicated target IDs in mapping table: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['C10orf2', 'CSRP2BP', 'MLL4', 'ODZ3']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['TCEB3C']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000256349']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['TCEB3C']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000226232']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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"Warning: query IDs not mapped to any target IDs excluded: 1\n"
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},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['HN1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['SLC35E2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['FAM21A', 'ODZ3']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['HEATR8', 'ENSG00000248710']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['HN1L', 'FLJ43860']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['TCEB3C']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000267385']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['KIAA1045']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['FAM21A']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000248710']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000258852']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000257921']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000254553']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MLL2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['HEATR8']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CCBP2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['FAM21A', 'ENSG00000260861']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MLL4']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['KIAA1804']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MLL4']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['B3GNT1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['DBC1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MLL2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['FLJ43860']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['FAM21A']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000261884']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['C2orf47', 'CD97']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MLL4']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['AGPAT9', 'ODZ3', 'ENSG00000260175']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MLL2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CD97']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['HN1', 'ENSG00000226232']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['FLJ22184']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['MLL2', 'TRAPPC2P1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CCRL1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['AZI1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000232637']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['FLJ22184']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MLL2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['AIM1', 'AZI1', 'MLL2', 'ENSG00000254553']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ADC']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['FAM21A']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['AIM1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000249209']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['KIAA1804']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 8\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"8 Hugo symbols not mapped to Entrez gene ID ['ABP1', 'AIM1', 'C11orf48', 'C2orf47', 'MLL4', 'ENSG00000187461', 'ENSG00000240127', 'ENSG00000260175']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['PPYR1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CXXC11']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000257033']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000251357']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000226232']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"CHOL\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 36 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort CHOL\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_CHOL.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"226 . 1550 Missense_Mutation point_mutation \n",
"215 PRSS1 5644 Missense_Mutation point_mutation \n",
"214 ZAN 7455 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"226 . (NA, NA) \n",
"215 . (NA, NA) \n",
"214 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"211 FOLR3 2352 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"211 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"118 . 728741 Missense_Mutation point_mutation \n",
"132 . 30816 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"118 . (NA, NA) \n",
"132 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"115 . 28891 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"115 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"129 . 50649 Missense_Mutation point_mutation \n",
"136 SH2B2 10603 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"129 . (NA, NA) \n",
"136 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"142 ANKRD13D 338692 Missense_Mutation point_mutation \n",
"129 ITGB3 3690 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"142 . (NA, NA) \n",
"129 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"175 MAP3K14 9020 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"175 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"96 TTC3 7267 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"96 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"146 . 388677 Missense_Mutation point_mutation \n",
"192 PCDH15 65217 Missense_Mutation point_mutation \n",
"178 TTYH3 80727 Missense_Mutation point_mutation \n",
"193 UHRF1 29128 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"146 . (NA, NA) \n",
"192 . (NA, NA) \n",
"178 . (NA, NA) \n",
"193 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"165 FRG1B 284802 Missense_Mutation point_mutation \n",
"166 FRG1B 284802 Missense_Mutation point_mutation \n",
"155 IWS1 55677 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"165 . (NA, NA) \n",
"166 . (NA, NA) \n",
"155 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"952 . 144535 Missense_Mutation point_mutation \n",
"956 . 220416 Missense_Mutation point_mutation \n",
"1000 . 285311 Missense_Mutation point_mutation \n",
"1116 C11orf31 280636 Missense_Mutation point_mutation \n",
"1121 COPG2 26958 Missense_Mutation point_mutation \n",
"1087 DNAH10 642797 Missense_Mutation point_mutation \n",
"1117 GPX2 2877 Missense_Mutation point_mutation \n",
"1118 ZNF274 10782 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"952 . (NA, NA) \n",
"956 . (NA, NA) \n",
"1000 . (NA, NA) \n",
"1116 . (NA, NA) \n",
"1121 . (NA, NA) \n",
"1087 . (NA, NA) \n",
"1117 . (NA, NA) \n",
"1118 . (NA, NA) \n",
"TCGA-W5-AA39-01A-11D-A417-09 CHOL 8 point mutations without a position 736 remain\n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"161 . 7203 Missense_Mutation point_mutation \n",
"174 INO80E 8479 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"161 . (NA, NA) \n",
"174 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"90 CPNE9 151835 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"90 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"273 . 400986 Missense_Mutation point_mutation \n",
"304 PRPF40A 55660 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"273 . (NA, NA) \n",
"304 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"125 ADIG 149685 Missense_Mutation point_mutation \n",
"116 GRK4 2868 In_Frame_Del point_mutation \n",
"117 SMAD5 4090 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"125 . (NA, NA) \n",
"116 . (NA, NA) \n",
"117 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"116 . 100129543 Missense_Mutation point_mutation \n",
"163 THSD7B 80731 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"116 . (NA, NA) \n",
"163 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"134 . 84443 Missense_Mutation point_mutation \n",
"137 ARHGAP25 9938 Missense_Mutation point_mutation \n",
"160 CECR2 27443 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"134 . (NA, NA) \n",
"137 . (NA, NA) \n",
"160 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"124 . 342850 Missense_Mutation point_mutation \n",
"112 CRTAM 56253 Missense_Mutation point_mutation \n",
"153 LILRB5 10990 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"124 . (NA, NA) \n",
"112 . (NA, NA) \n",
"153 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"185 . 91646 Missense_Mutation point_mutation \n",
"221 DNAH11 8701 Missense_Mutation point_mutation \n",
"219 FRG1B 284802 Missense_Mutation point_mutation \n",
"220 FRG1B 284802 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"185 . (NA, NA) \n",
"221 . (NA, NA) \n",
"219 . (NA, NA) \n",
"220 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"105 MACF1 23499 Missense_Mutation point_mutation \n",
"148 PCDH15 65217 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"105 . (NA, NA) \n",
"148 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"142 . 400986 Missense_Mutation point_mutation \n",
"139 ANKRD30BL 554226 Missense_Mutation point_mutation \n",
"129 NBPF1 55672 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"142 . (NA, NA) \n",
"139 . (NA, NA) \n",
"129 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"183 FRG1B 284802 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"183 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"145 MIR548F5 26960 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"145 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"189 PRKDC 5591 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"189 . (NA, NA) \n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"190 PCSK6 5046 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"190 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"111 . 131034 Missense_Mutation point_mutation \n",
"142 METTL8 79828 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"111 . (NA, NA) \n",
"142 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"158 MAPK6 5597 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"158 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"101 . 319089 Missense_Mutation point_mutation \n",
"94 FOXRED1 55572 Missense_Mutation point_mutation \n",
"117 SPEF2 79925 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"101 . (NA, NA) \n",
"94 . (NA, NA) \n",
"117 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"115 . 728841 Missense_Mutation point_mutation \n",
"128 . 400986 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"115 . (NA, NA) \n",
"128 . (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"88 . 80167 Missense_Mutation point_mutation \n",
"108 . 400986 Missense_Mutation point_mutation \n",
"98 TSPAN14 81619 Missense_Mutation point_mutation \n",
"\n",
" AAChange aa_pos \n",
"88 . (NA, NA) \n",
"108 . (NA, NA) \n",
"98 . (NA, NA) \n",
"preprocessed maf 124 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort THYM\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_THYM.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"THYM\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['MT-ATP6', 'MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ATP6']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000260415']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND6']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['LOC101930102', 'MT-ND6']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000263264']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000176984']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND6']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['CSRP2BP', 'ENSG00000243501', 'ENSG00000269089']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND6']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND4L']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['MT-CO1', 'MT-ND5']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['AIM1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000256530']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"UCEC\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 249 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort UCEC\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_UCEC.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"SKCM\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 346 fies;\t\traw maf: 369 files\n",
"select raw maf file for cohort SKCM\n",
"use path ../../TCGA/mutations/data_raw/gdac.broadinstitute.org_SKCM.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0/\n",
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (38,50,67,81,82,83,84) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n",
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (38,50,81,82,83,84) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"PRAD\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 333 fies;\t\traw maf: 500 files\n",
"select raw maf file for cohort PRAD\n",
"use path ../../TCGA/mutations/data_raw/gdac.broadinstitute.org_PRAD.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0/\n",
"/home/olya/miniconda2/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2714: DtypeWarning: Columns (38,67,81,82,83,84) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"LIHC\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 199 fies;\t\traw maf: 374 files\n",
"select raw maf file for cohort LIHC\n",
"use path ../../TCGA/mutations/data_raw/gdac.broadinstitute.org_LIHC.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"ESCA\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 186 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort ESCA\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_ESCA.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['AIM1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000237452', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000268194']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000257743']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC100509091']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000257743']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000197182', 'ENSG00000228768', 'ENSG00000232748']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000145965', 'ENSG00000242628', 'ENSG00000257743']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000205018', 'MT-CO1', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000167765']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000255537', 'MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000257743']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 7\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"7 Hugo symbols not mapped to Entrez gene ID ['AGPAT9', 'AZI1', 'ENSG00000212999', 'ENSG00000249428', 'ENSG00000260415', 'ENSG00000267848', 'ENSG00000268241']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['MT-ATP6', 'MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000167765']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000232866']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000212884']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['B3GNT1', 'ENSG00000212857', 'ENSG00000268059', 'MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC101928664']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000187811', 'ENSG00000267848', 'MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['AZI1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['MT-CO1', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000234719']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['CSRP2BP', 'ENSG00000231171', 'ENSG00000263020']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000212857', 'ENSG00000228532']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['B3GNT1', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs mapping to duplicated target IDs in mapping table: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000255622', 'ENSG00000257743', 'FLJ22184']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000212857', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000254469', 'MT-CO1', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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},
{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000248801', 'ENSG00000257057', 'ENSG00000264222']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['AIM1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000253172', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000226524', 'ENSG00000259455', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['HN1L']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000176593']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000217825']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000212857', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000269490']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['FLJ46361']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC101930611']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['LOC100996779', 'ENSG00000217825', 'ENSG00000267848', 'ENSG00000269175']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"CESC\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 195 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort CESC\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_CESC.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"THCA\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 405 fies;\t\traw maf: 505 files\n",
"select raw maf file for cohort THCA\n",
"use path ../../TCGA/mutations/data_raw/gdac.broadinstitute.org_THCA.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['RP11-113D6.10']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"DLBC\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 49 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort DLBC\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_DLBC.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"GBM\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 291 fies;\t\traw maf: 291 files\n",
"select processed maf file for cohort GBM\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_GBM.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"UCS\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 58 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort UCS\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_UCS.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"LAML\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 198 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort LAML\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_LAML.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n",
"1 Hugo symbols not mapped to Entrez gene ID ['LOC100132232']\n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"18 FLT3 2322 In_Frame_Ins point_mutation \n",
"\n",
" amino_acid_change aa_pos \n",
"18 in_frame_ins (NA, NA) \n",
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CYB']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['uc004amh.1']\n",
"4 Hugo symbols not mapped to Entrez gene ID ['LOC100130734', 'LOC100132903', 'LOC387761', 'LOC727878']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC100131040']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000216522']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC100128077']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['uc002rsf.1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC728896']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CYB']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC727895']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CYB']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CYB']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['MT-ND1', 'MT-ND4', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['MT-CYB', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['PRG-3', 'ENSG00000211619']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['NOTCH2NL', 'LOC200493']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC100129901']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['MLL2', 'LOC100132800', 'LOC100133684', 'MT-CO3']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CYB']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['EFTUD1', 'LOC730032']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['LOC100129218', 'ENSG00000103832']\n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"2 FLT3 2322 In_Frame_Ins point_mutation \n",
"\n",
" amino_acid_change aa_pos \n",
"2 in_frame_ins (NA, NA) \n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['LOC644504', 'ENSG00000214135']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['LOC100132713', 'LOC100134687']\n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"16 FLT3 2322 In_Frame_Ins point_mutation \n",
"\n",
" amino_acid_change aa_pos \n",
"16 in_frame_ins (NA, NA) \n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['FLJ43860', 'MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['MT-ND5', 'uc001vvs.1']\n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"16 FLT3 2322 In_Frame_Ins point_mutation \n",
"\n",
" amino_acid_change aa_pos \n",
"16 in_frame_ins (NA, NA) \n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000198229']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000211894']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CO3']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC100133915']\n",
"2"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo symbols not mapped to Entrez gene ID ['LOC100133718', 'LOC730167']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['LOC100133292']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000215720', 'ENSG00000220279']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC100128371']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000124399']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['FLJ22167']\n",
"1"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo symbols not mapped to Entrez gene ID ['MT-ATP6']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['ODZ3', 'LOC100128989', 'LOC100129218']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['LOC257039']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC100133655']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC100132495']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC100131699']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC100132800']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000163098']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['LOC644992']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['MT-CO3', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['uc004ewl.1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000204989']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['PRAMEF16']\n",
"1"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"HNSC\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo symbols not mapped to Entrez gene ID ['LOC100128744']\n",
"preprocessed maf 280 fies;\t\traw maf: 513 files\n",
"select raw maf file for cohort HNSC\n",
"use path ../../TCGA/mutations/data_raw/gdac.broadinstitute.org_HNSC.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"PAAD\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 151 fies;\t\traw maf: 186 files\n",
"select raw maf file for cohort PAAD\n",
"use path ../../TCGA/mutations/data_raw/gdac.broadinstitute.org_PAAD.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"LUAD\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 231 fies;\t\traw maf: 544 files\n",
"select raw maf file for cohort LUAD\n",
"use path ../../TCGA/mutations/data_raw/gdac.broadinstitute.org_LUAD.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"UVM\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 81 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort UVM\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_UVM.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"10 REC8 9985 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"10 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"17 TEP1 7011 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"17 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"16 ABCB4 5244 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"16 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"7 AP1G2 8906 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"7 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"16 E2F7 144455 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"16 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"8 P2RX1 5023 Missense_Mutation point_mutation \n",
"9 RGL4 266747 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"8 NA (NA, NA) \n",
"9 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"14 RYR2 6262 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"14 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"3 NEBL 10529 Missense_Mutation point_mutation \n",
"8 RSG1 79363 Missense_Mutation point_mutation \n",
"0 ZMYM3 9203 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"3 NA (NA, NA) \n",
"8 NA (NA, NA) \n",
"0 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"3 OLFM1 10439 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"3 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"1 MRAS 22808 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"1 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"6 BAP1 8314 Missense_Mutation point_mutation \n",
"8 VSIG10 54621 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"6 NA (NA, NA) \n",
"8 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"6 DLGAP5 9787 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"6 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"18 COMMD4 54939 Missense_Mutation point_mutation \n",
"13 MRPS24 64951 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"18 NA (NA, NA) \n",
"13 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"14 MYO1C 4641 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"14 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"2 ITPR2 3709 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"2 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"15 ANO10 55129 Missense_Mutation point_mutation \n",
"9 MAPK8IP3 23162 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"15 NA (NA, NA) \n",
"9 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"14 ZNF654 55279 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"14 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"3 PRDM2 7799 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"3 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"2 RTTN 25914 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"2 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"1 ATG9A 79065 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"1 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"2 ZNF525 170958 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"2 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"10 RPS9 6203 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"10 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"21 ZNF839 55778 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"21 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"13 LRP1 4035 Missense_Mutation point_mutation \n",
"6 MDN1 23195 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"13 NA (NA, NA) \n",
"6 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"1 HTR1E 3354 Missense_Mutation point_mutation \n",
"13 SYTL3 94120 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"1 NA (NA, NA) \n",
"13 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"16 MYO15A 51168 Missense_Mutation point_mutation \n",
"9 PTCHD1 139411 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"16 NA (NA, NA) \n",
"9 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"6 RAD54L2 23132 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"6 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"530 DPP4 1803 Missense_Mutation point_mutation \n",
"403 GABRD 2563 Missense_Mutation point_mutation \n",
"46 ROR2 4920 Missense_Mutation point_mutation \n",
"570 XAB2 56949 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"530 NA (NA, NA) \n",
"403 NA (NA, NA) \n",
"46 NA (NA, NA) \n",
"570 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"6 MYO3B 140469 Missense_Mutation point_mutation \n",
"15 OBSCN 84033 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"6 NA (NA, NA) \n",
"15 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"16 PPM1J 333926 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"16 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"6 COQ2 27235 Missense_Mutation point_mutation \n",
"8 RP11-1084J3.4 114899 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"6 NA (NA, NA) \n",
"8 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"5 ANKAR 150709 Missense_Mutation point_mutation \n",
"7 ANKAR 150709 Missense_Mutation point_mutation \n",
"1 BBX 56987 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"5 NA (NA, NA) \n",
"7 NA (NA, NA) \n",
"1 NA (NA, NA) \n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"13 KATNB1 10300 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"13 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"21 SEMA5A 9037 Missense_Mutation point_mutation \n",
"3 TNPO3 23534 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"21 NA (NA, NA) \n",
"3 NA (NA, NA) \n",
" Hugo_Symbol Entrez_gene_ID Variant_Classification function \\\n",
"6 PKP3 11187 Missense_Mutation point_mutation \n",
"\n",
" Protein_Change aa_pos \n",
"6 NA (NA, NA) \n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"SARC\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 248 fies;\t\traw maf: 0 files\n",
"select processed maf file for cohort SARC\n",
"use path ../../TCGA/mutations/data/gdac.broadinstitute.org_SARC.Mutation_Packager_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000234978', 'ENSG00000269688', 'ENSG00000272231']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 8\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"8 Hugo symbols not mapped to Entrez gene ID ['AZI1', 'ENSG00000205821', 'ENSG00000221136', 'ENSG00000222717', 'ENSG00000261616', 'ENSG00000270726', 'MT-CO1', 'MT-ND5']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000250992']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000203849']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['DH17', 'ENSG00000215958', 'ENSG00000237357', 'MT-RNR2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221704', 'ENSG00000258727']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000230850']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['CNTP5', 'DH7', 'ENSG00000185710']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['MT-CO1', 'T10']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['CAC2D1', 'DH11', 'ENSG00000215398', 'ENSG00000234719']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['CHR9', 'ENSG00000215958', 'ENSG00000237452']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n",
"Warning: query IDs not mapped to any target IDs excluded: 6\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['DJA4', 'EM', 'ENSG00000268673', 'PSB', 'SP91']\n",
"6 Hugo symbols not mapped to Entrez gene ID ['LOC100507033', 'ENSG00000267219', 'ENSG00000269939', 'ENSG00000273433', 'MT-ATP8', 'PEPLD']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['ENSG00000206567', 'ENSG00000221280', 'ENSG00000226716', 'ENSG00000265803', 'ENSG00000268823']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000262712']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221741', 'ENSG00000222586', 'T10']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['LOC101929847', 'ENSG00000221295']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['ALAD2', 'CNTP3', 'ENSG00000215979', 'ENSG00000221659', 'ENSG00000259241']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000252677']\n",
"3 "
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Hugo symbols not mapped to Entrez gene ID ['ENSG00000214614', 'MT-CO1', 'MT-RNR2']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['CAC1A', 'DJC1', 'ENSG00000225946']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221704']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 7\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"7 Hugo symbols not mapped to Entrez gene ID ['DH2', 'ENSG00000201913', 'ENSG00000214581', 'ENSG00000215022', 'ENSG00000221295', 'ENSG00000221388', 'ENSG00000272667']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['LOC101930494', 'DH2', 'DJB3', 'KC5', 'ST6GALC4']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000173213', 'ENSG00000237281', 'ENSG00000265002']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['EB1BP2', 'ENSG00000223697', 'ENSG00000256616', 'ENSG00000270726', 'PLX2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n",
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['DH10', 'ENSG00000221684', 'ENSG00000264299', 'ENSG00000266657']\n",
"4 Hugo symbols not mapped to Entrez gene ID ['ENSG00000196589', 'ENSG00000221235', 'ENSG00000254551', 'ENSG00000255200']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['GT1', 'CAC1S', 'ENSG00000232274', 'ENSG00000253200']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['LOC100293748', 'ENSG00000161103', 'ENSG00000227175', 'ENSG00000233207', 'IFR1']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['DH2', 'FLJ46361', 'RG2']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['APC4', 'ENSG00000251199', 'ENSG00000265194']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221684', 'ENSG00000256616']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 9\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"9 Hugo symbols not mapped to Entrez gene ID ['AHK2', 'CAC1A', 'ENSG00000203849', 'ENSG00000215923', 'ENSG00000215954', 'ENSG00000224643', 'ENSG00000233825', 'ENSG00000258437', 'ENSG00000266999']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['CSGALCT1', 'DJB3', 'RG2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['LOC101928102', 'DH11', 'ENSG00000221011', 'ENSG00000234978', 'ENSG00000267260']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['DJB8-AS1', 'ENSG00000223063', 'ENSG00000267045']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['CAC2D4', 'ENSG00000235852', 'ENSG00000236911', 'MT-RNR1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 7\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"7 Hugo symbols not mapped to Entrez gene ID ['CAC1E', 'ENSG00000205745', 'ENSG00000221280', 'ENSG00000259455', 'ENSG00000269939', 'FLJ26850', 'SI3']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['AHK', 'CNTP3B', 'ENSG00000204398', 'ENSG00000244306', 'ENSG00000256982', 'ENSG00000263378']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 21\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"21 Hugo symbols not mapped to Entrez gene ID ['CAC1S', 'DH10', 'DH17', 'DH6', 'DH7', 'ENSG00000188477', 'ENSG00000189275', 'ENSG00000205663', 'ENSG00000215958', 'ENSG00000221137', 'ENSG00000221379', 'ENSG00000234722', 'ENSG00000235772', 'ENSG00000237265', 'ENSG00000256982', 'ENSG00000257057', 'ENSG00000257829', 'ENSG00000260628', 'ENSG00000267943', 'KP2', 'RSEL']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
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"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['LOC101928703', 'ENSG00000216020', 'ENSG00000221279']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['CAC1A', 'CAC1C', 'ENSG00000200485']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
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"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000196096', 'ENSG00000244327']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['DH7', 'RSE8']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
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"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000258727']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
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"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['CAC1A', 'CNTP3', 'ENSG00000221395', 'ENSG00000266885', 'ENSG00000267040']\n"
]
},
{
"name": "stdout",
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"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
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"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000216194']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['AHK', 'ENSG00000228436', 'ENSG00000228532', 'ENSG00000229743', 'ENSG00000260628', 'ENSG00000260973']\n",
"2"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo symbols not mapped to Entrez gene ID ['ENSG00000216089', 'LINC00846']\n",
"5 Hugo symbols not mapped to Entrez gene ID ['CNTP5', 'DH2', 'ENSG00000161103', 'ENSG00000221544', 'ENSG00000269690']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 8\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221664', 'ENSG00000227175', 'R5-8SP6']\n",
"8 Hugo symbols not mapped to Entrez gene ID ['TCEB3C', 'ENSG00000171658', 'ENSG00000212939', 'ENSG00000215527', 'ENSG00000249149', 'ENSG00000257769', 'ENSG00000257931', 'ENSG00000261759']\n",
"1"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo symbols not mapped to Entrez gene ID ['APC1']\n",
"4 Hugo symbols not mapped to Entrez gene ID ['CAC1B', 'DH5', 'ENSG00000255487', 'GZ']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['DJC11', 'RSE2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000216004', 'ENSG00000233434', 'ENSG00000240253']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000258704']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['ENSG00000167765', 'ENSG00000231345', 'ENSG00000250910', 'ENSG00000267075']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['CAC1H', 'ENSG00000188971']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['LOC101928729', 'ENSG00000263120', 'ENSG00000267353']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221492', 'ENSG00000244227']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['CGB', 'ENSG00000239179', 'MT-RNR2', 'MT-TL1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['CHR4', 'ENSG00000226668', 'ENSG00000261546']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['LOC101928780', 'DJC13', 'ENSG00000248115', 'ENSG00000268032']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 9\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"9 Hugo symbols not mapped to Entrez gene ID ['ADC', 'CTN2', 'ENSG00000242474', 'ENSG00000254665', 'ENSG00000255384', 'ENSG00000260213', 'ENSG00000267387', 'FLJ22184', 'TIG']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000225241']\n",
"4 Hugo symbols not mapped to Entrez gene ID ['ENSG00000212768', 'ENSG00000221121', 'ENSG00000233836', 'R5-8SP6']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['DH3', 'DH5', 'NMT3']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['CAC1G', 'ENSG00000203849', 'MT-RNR2']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000216020', 'ENSG00000226145', 'ENSG00000258364']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['AHK', 'AHK2']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000211996', 'ENSG00000214581', 'ENSG00000234222']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['DJC13', 'ENSG00000221810', 'ENSG00000273192']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['ENSG00000216191', 'ENSG00000218416', 'ENSG00000221280', 'ENSG00000233863', 'ENSG00000260411', 'PLX2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221118', 'ENSG00000226232', 'ENSG00000268301']\n",
"1"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo symbols not mapped to Entrez gene ID ['AHK2']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221684', 'P1L3']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000236233', 'ENSG00000270012']\n",
"5 Hugo symbols not mapped to Entrez gene ID ['APC1', 'ENSG00000216191', 'ENSG00000228302', 'MT-CO1', 'MT-TS2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n",
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['LOC101929847', 'ENSG00000205746', 'ENSG00000216113', 'ENSG00000269243', 'MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 9\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"9 Hugo symbols not mapped to Entrez gene ID ['TCEB3CL', 'CAC1G', 'DH8', 'DJC22', 'ENSG00000221104', 'ENSG00000226738', 'ENSG00000242111', 'ENSG00000259037', 'KC1']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['CAC1A']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs mapping to duplicated target IDs in mapping table: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 51\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"51 Hugo symbols not mapped to Entrez gene ID ['STRA13', 'LOC101930008', 'LOC440157', 'CA', 'CAC1C-AS1', 'CAC1D', 'CAC1S', 'CAC2D1', 'CNTP2', 'CTN2', 'DH14', 'DH3', 'DH5', 'DH6', 'DH7', 'DJB13', 'DJB3', 'DJC13', 'EH', 'ENSG00000188477', 'ENSG00000203849', 'ENSG00000219926', 'ENSG00000221653', 'ENSG00000225261', 'ENSG00000227175', 'ENSG00000228980', 'ENSG00000231171', 'ENSG00000231512', 'ENSG00000232274', 'ENSG00000234810', 'ENSG00000234921', 'ENSG00000235772', 'ENSG00000235881', 'ENSG00000250026', 'ENSG00000251273', 'ENSG00000251429', 'ENSG00000258559', 'ENSG00000260874', 'ENSG00000261720', 'ENSG00000267575', 'ENSG00000269352', 'ENSG00000269495', 'ENSG00000269533', 'ENSG00000272084', 'ENSG00000273189', 'FLJ33360', 'MGC34034', 'PLX2', 'SERPI3', 'SP91', 'V3']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 9\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"9 Hugo symbols not mapped to Entrez gene ID ['DH7', 'ENSG00000224363', 'ENSG00000237452', 'ENSG00000245156', 'ENSG00000252258', 'ENSG00000257434', 'KP3', 'MT-CO1', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000271894']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 7\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"7 Hugo symbols not mapped to Entrez gene ID ['CAC1H', 'CHR9', 'DJC8', 'ENSG00000187695', 'ENSG00000230333', 'ENSG00000257057', 'ENSG00000272231']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['CAC1F', 'ENSG00000254553', 'ENSG00000257743', 'ENSG00000271959']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['ENSG00000205918', 'ENSG00000216054', 'ENSG00000226145', 'ENSG00000264576', 'GI2', 'MT-RNR1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n",
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['ENSG00000173213', 'ENSG00000215067', 'ENSG00000215933', 'ENSG00000221096', 'ENSG00000238737', 'ENSG00000251226']\n",
"5 Hugo symbols not mapped to Entrez gene ID ['LOC100128374', 'DH14', 'ENSG00000215941', 'ENSG00000236295', 'ENSG00000272356']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['101928757', 'ENSG00000216073', 'ENSG00000221281']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000213132', 'ENSG00000234722']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['LOC100293748', 'ENSG00000216113', 'ENSG00000221684', 'MT-RNR2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['ENSG00000215972', 'ENSG00000227082', 'ENSG00000250186', 'ENSG00000273433', 'IF16']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000226113', 'ENSG00000266060', 'MT-RNR1']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000203849', 'MT-ND5', 'MT-RNR2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['DH5', 'ENSG00000223291', 'ENSG00000243175', 'ENSG00000261393', 'ENSG00000272885']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['LOC101060604', 'DJC13', 'EH', 'ENSG00000249149', 'ENSG00000264057']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 7\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"7 Hugo symbols not mapped to Entrez gene ID ['ENSG00000215954', 'ENSG00000221280', 'ENSG00000222732', 'ENSG00000256249', 'ENSG00000265289', 'ENSG00000271959', 'MT-RNR2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 11\n",
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"11 Hugo symbols not mapped to Entrez gene ID ['CTN2', 'DH8', 'ENSG00000180458', 'ENSG00000215933', 'ENSG00000221279', 'ENSG00000221317', 'ENSG00000221388', 'ENSG00000221664', 'ENSG00000251966', 'ENSG00000257395', 'ENSG00000259241']\n",
"5 Hugo symbols not mapped to Entrez gene ID"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" ['ENSG00000221319', 'ENSG00000237234', 'ENSG00000238411', 'ENSG00000268985', 'GLU']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['CAC1S', 'ENSG00000215953', 'ENSG00000268032']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['CNTP4', 'ENSG00000227082', 'ENSG00000259605', 'ENSG00000268573', 'MT-CO1']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['CTN2', 'ENSG00000262903']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['DH12', 'ENSG00000216191', 'ENSG00000229481', 'ENSG00000259455', 'ENSG00000259966', 'I']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['LOC100996870', '101928757', 'DH10']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 8\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"8 Hugo symbols not mapped to Entrez gene ID ['CAC1F', 'DH11', 'ENSG00000224631', 'ENSG00000230615', 'ENSG00000232274', 'ENSG00000245330', 'ENSG00000268032', 'ST6GALC3']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['LOC100507033', 'DH7', 'ENSG00000222033', 'ENSG00000260628', 'ENSG00000272913']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000263120', 'ENSG00000268812']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000244227']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['ENSG00000216127', 'ENSG00000221395', 'ENSG00000265209', 'ENSG00000267801']\n",
"3"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 11\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo symbols not mapped to Entrez gene ID ['DH14', 'ENSG00000249237', 'FLJ40448']\n",
"11 Hugo symbols not mapped to Entrez gene ID ['GL', 'DF5', 'ENSG00000184774', 'ENSG00000203849', 'ENSG00000216173', 'ENSG00000221279', 'ENSG00000221388', 'ENSG00000224516', 'ENSG00000251273', 'MT-TY', 'TSRE1']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000234613', 'ENSG00000237452', 'SERPI10']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['DH5', 'ENSG00000273199']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
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"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['CAC1D', 'ENSG00000215958']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
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"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['LOC101928787', 'MT-RNR1']\n",
"2 "
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n",
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
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"text": [
"Hugo symbols not mapped to Entrez gene ID ['DH9', 'FLJ41200']\n",
"5 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221810', 'ENSG00000259455', 'ENSG00000269890', 'ENSG00000273312', 'KIAA1045']\n",
"4 Hugo symbols not mapped to Entrez gene ID ['LOC101928921', 'DH6', 'ENSG00000221145', 'ENSG00000248115']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
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"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000234978']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
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"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['CAC1F', 'ENSG00000183154', 'ENSG00000233002', 'ENSG00000254990', 'ENSG00000259668']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 7\n"
]
},
{
"name": "stderr",
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"text": [
"7 Hugo symbols not mapped to Entrez gene ID ['DH5', 'ENSG00000197210', 'ENSG00000226145', 'ENSG00000231611', 'ENSG00000255384', 'FLJ45139', 'IF8']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
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"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000245482']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 8\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
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"text": [
"8 Hugo symbols not mapped to Entrez gene ID ['LOC101927648', 'LOC101930657', 'AHK2', 'CNTP2', 'ENSG00000215933', 'ENSG00000215953', 'ENSG00000259521', 'ENSG00000267865']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000216166', 'ENSG00000232274', 'ENSG00000261351']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['AZI1', 'DH2', 'DI2', 'ENSG00000268366']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['CHR4']\n",
"5 Hugo symbols not mapped to Entrez gene ID ['ENSG00000205215', 'ENSG00000268081', 'ENSG00000269688', 'ENSG00000272485', 'MT-RNR2']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
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"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['CNTP5', 'ENSG00000256616']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['A40']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['ENSG00000229047', 'ENSG00000238009', 'ENSG00000244151', 'ENSG00000255641', 'KC5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
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"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['FLJ20444']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 8\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
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"text": [
"8 Hugo symbols not mapped to Entrez gene ID ['LOC101928921', 'DAF3', 'DJA3', 'ENSG00000204398', 'ENSG00000214105', 'ENSG00000229953', 'ENSG00000249430', 'MT-CO1']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000212952', 'ENSG00000221591', 'FLJ40448']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['DH9', 'ENSG00000272231']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
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"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000232274', 'ENSG00000235999']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['CAC1C', 'CNTP5', 'ENSG00000166104', 'ENSG00000177699', 'ENSG00000215346', 'ENSG00000272231']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-RNR2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221664', 'ENSG00000239012', 'MT-ATP6']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['IF1']\n"
]
},
{
"name": "stdout",
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"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['CD97', 'DJB11', 'ENSG00000229852', 'ENSG00000271828', 'RSE10', 'V3']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['ENSG00000216089', 'ENSG00000237452', 'ENSG00000254592', 'ENSG00000257743', 'ENSG00000267660']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000215954']\n",
"4 Hugo symbols not mapped to Entrez gene ID ['CNTP4', 'ENSG00000228506', 'PLX3', 'RSET2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n",
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['AIM1', 'DH5', 'ENSG00000221244', 'ENSG00000251226']\n",
"5"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo symbols not mapped to Entrez gene ID ['GS', 'ENSG00000227175', 'ENSG00000232274', 'ENSG00000273000', 'ST6GALC5']\n",
"4 Hugo symbols not mapped to Entrez gene ID ['AHK2', 'DH8', 'ENSG00000204792', 'ENSG00000226849']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['ENSG00000179253', 'ENSG00000232274', 'ENSG00000257434', 'ENSG00000267601']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['CHR7', 'ENSG00000201913', 'ENSG00000227407']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 9\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"9 Hugo symbols not mapped to Entrez gene ID ['LOC101929948', 'ALAD2', 'CAC1B', 'CAC1F', 'DH11', 'DH6', 'DH9', 'ENSG00000223164', 'IF14']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000216089']"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n",
"4 Hugo symbols not mapped to Entrez gene ID ['LOC101927091', 'ENSG00000167765', 'ENSG00000253629', 'ENSG00000263120']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000264542', 'MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000257433']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['DH11', 'DH6', 'ENSG00000253381']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['CAC1C', 'DH14', 'ENSG00000185710', 'ENSG00000215941', 'RSEK']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000215941', 'IF17']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 12\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"12 Hugo symbols not mapped to Entrez gene ID ['LOC101929847', 'AHK', 'CSPG4P8', 'ENSG00000215941', 'ENSG00000221672', 'ENSG00000223200', 'ENSG00000228463', 'ENSG00000236233', 'ENSG00000261238', 'ENSG00000266535', 'ENSG00000268889', 'V3']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['BP2', 'ENSG00000264151', 'ST6GALC3']\n",
"3 Hugo symbols not mapped to Entrez gene ID ['DH14', 'DI2', 'SERPI11']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221415', 'ENSG00000270433']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['DH9', 'ENSG00000226145', 'ENSG00000272231']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 18\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"18 Hugo symbols not mapped to Entrez gene ID ['AIM1', 'AHK2', 'CAC1F', 'CSGALCT1', 'CTN2', 'DH9', 'DJC17', 'DJC24', 'DK2', 'ENSG00000188474', 'ENSG00000204038', 'ENSG00000221664', 'ENSG00000223579', 'ENSG00000232675', 'ENSG00000252176', 'ENSG00000272625', 'FLJ27255', 'KC5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000223730', 'MT-RNR2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['AHK', 'DJC5B', 'ENSG00000221684', 'ENSG00000254553', 'MIR3118-6', 'MT-TF']\n",
"2 Hugo symbols not mapped to Entrez gene ID "
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"['CAC1B', 'ENSG00000272231']\n",
"4 Hugo symbols not mapped to Entrez gene ID ['ENSG00000222032', 'ENSG00000234277', 'ENSG00000251273', 'RSEL']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000215941', 'ENSG00000215976']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-RNR2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n",
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['CNTP2', 'DJC13', 'ENSG00000236432', 'ENSG00000264164']\n",
"4 Hugo symbols not mapped to Entrez gene ID ['ENSG00000184566', 'ENSG00000216154', 'ENSG00000230615', 'ENSG00000270726']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 8\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"8 Hugo symbols not mapped to Entrez gene ID ['LOC100128374', 'AHK2', 'CAC1B', 'CAC1I', 'ENSG00000226145', 'ENSG00000242288', 'ENSG00000254967', 'FLJ44006']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['KC1']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000214397', 'FLJ46361']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['DH17', 'ENSG00000200294', 'ENSG00000221732']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000224505', 'PLX2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CNTP3']\n",
"4 Hugo symbols not mapped to Entrez gene ID ['LOC440157', 'DJB2', 'ENSG00000215933', 'ENSG00000221474']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n",
"Warning: query IDs not mapped to any target IDs excluded: 6\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['CAC1I', 'ENSG00000203849', 'ENSG00000221121', 'ENSG00000221281', 'ENSG00000232274', 'ENSG00000267943']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000215954', 'ENSG00000230615']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['DH17', 'ENSG00000265002']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['ENSG00000218739', 'ENSG00000221279', 'ENSG00000221280', 'ENSG00000221307', 'ENSG00000255193', 'KC1']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000272231', 'MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 2"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000215941', 'ENSG00000265865']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000267075', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['DH8', 'ENSG00000221684']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['DH3', 'ENSG00000221696', 'ENSG00000258944', 'ENSG00000268366']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['A60', 'CTN2', 'DH7']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['CTN3', 'DH5', 'ENSG00000263120']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-RNR2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 7\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"7 Hugo symbols not mapped to Entrez gene ID ['CAC1C', 'DH8', 'ENSG00000211510', 'ENSG00000215941', 'ENSG00000221388', 'IF1', 'KC3']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['DH5', 'DH6', 'ENSG00000251273', 'ENSG00000259241', 'ENSG00000267260']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221672', 'ENSG00000221704', 'R5-8SP6']\n",
"4 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221280', 'ENSG00000233002', 'ENSG00000244306', 'MT-ND6']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['DH17-AS1', 'DH2', 'ENSG00000205018', 'ENSG00000215941', 'ENSG00000258661', 'ENSG00000264222']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000259241']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 11\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"11 Hugo symbols not mapped to Entrez gene ID ['AHK', 'CHR3', 'DH17', 'ENSG00000204038', 'ENSG00000232274', 'ENSG00000233145', 'ENSG00000242539', 'ENSG00000244306', 'ENSG00000257042', 'ENSG00000273433', 'PLX1']\n",
"4 Hugo symbols not mapped to Entrez gene ID ['ENSG00000215941', 'ENSG00000221664', 'ENSG00000231486', 'ENSG00000259479']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n",
"Warning: query IDs not mapped to any target IDs excluded: 5\n",
"Warning: query IDs not mapped to any target IDs excluded: 6\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['CAC1A', 'CAC1G', 'CNTP3', 'ENSG00000222717', 'ENSG00000228980']\n",
"6 Hugo symbols not mapped to Entrez gene ID ['AZI1', 'ENSG00000221219', 'ENSG00000221307', 'ENSG00000250026', 'ENSG00000270726', 'MT-RNR1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000249275', 'KATL1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000227719', 'ENSG00000264299']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000216116', 'ENSG00000254913', 'ENSG00000263606']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['DH14', 'ENSG00000266490', 'ENSG00000269988']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 92\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"92 Hugo symbols not mapped to Entrez gene ID ['ADC', 'PA', 'PSA', 'STRA13', 'LOC100996735', 'LOC101929518', '101928757', 'AHK', 'AHK2', 'BACH1-IT1', 'CA', 'CAC1A', 'CAC1E', 'CAC1I', 'CAC1S', 'CAC2D3', 'CHR9', 'CTN3', 'DF5', 'DH10', 'DH11', 'DH17', 'DH5', 'DH8', 'DH9', 'DJB8', 'DSE1L2', 'EB1BP2', 'ENSG00000166104', 'ENSG00000173213', 'ENSG00000177553', 'ENSG00000182873', 'ENSG00000184566', 'ENSG00000187812', 'ENSG00000204038', 'ENSG00000205018', 'ENSG00000207187', 'ENSG00000215023', 'ENSG00000221335', 'ENSG00000224113', 'ENSG00000224631', 'ENSG00000225891', 'ENSG00000228998', 'ENSG00000229839', 'ENSG00000230578', 'ENSG00000230615', 'ENSG00000231437', 'ENSG00000234232', 'ENSG00000234978', 'ENSG00000235881', 'ENSG00000238129', 'ENSG00000239674', 'ENSG00000240401', 'ENSG00000247121', 'ENSG00000249502', 'ENSG00000250046', 'ENSG00000254551', 'ENSG00000254571', 'ENSG00000254815', 'ENSG00000254844', 'ENSG00000255200', 'ENSG00000256209', 'ENSG00000257494', 'ENSG00000258017', 'ENSG00000259426', 'ENSG00000260973', 'ENSG00000261709', 'ENSG00000262732', 'ENSG00000263738', 'ENSG00000263887', 'ENSG00000265899', 'ENSG00000267688', 'ENSG00000268650', 'ENSG00000268864', 'ENSG00000269636', 'ENSG00000269888', 'ENSG00000272017', 'ENSG00000272849', 'ENSG00000273106', 'FLJ27255', 'KC4', 'KP1', 'NIPSP3B', 'PLX4', 'RSE10', 'SERPI7', 'SP29', 'TIG', 'TIGL1', 'TRU1AP', 'TTLL10-AS1', 'V3']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000253334', 'LCN']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 25\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"25 Hugo symbols not mapped to Entrez gene ID ['EFTUD1', 'GS', 'CAC1E', 'CNTP5', 'CTN1', 'DAF1', 'DH17', 'DJC10', 'ENSG00000187812', 'ENSG00000203496', 'ENSG00000203849', 'ENSG00000223804', 'ENSG00000233487', 'ENSG00000237265', 'ENSG00000249509', 'ENSG00000258908', 'ENSG00000261759', 'ENSG00000265002', 'ENSG00000266817', 'ENSG00000267561', 'ENSG00000269895', 'ENSG00000271959', 'FLJ46361', 'SERPI1', 'ST6GALC1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221734', 'ENSG00000255622', 'ENSG00000261200']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000216102', 'R5-8SP6']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n",
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['FAM21A', 'ENSG00000261720', 'ENSG00000267749']\n",
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000221280', 'ENSG00000267075']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['DH9', 'ENSG00000221281', 'ENSG00000265002', 'ENSG00000268845', 'LCN']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['LOC101929847', 'DH10', 'ENSG00000221388']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000237357', 'ENSG00000266156']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['LOC101927958', 'DJC8', 'ENSG00000262112', 'KIAA1804']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['CAC1H', 'CHR5', 'DH9', 'ENSG00000207207']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000257434']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['LOC101930284', 'ENSG00000203849', 'ENSG00000221156']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['DH14', 'KC4', 'MT-RNR2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['CAC1H', 'DH8', 'ENSG00000204398', 'ENSG00000244227', 'ENSG00000258973', 'ENSG00000266008']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 8\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"8 Hugo symbols not mapped to Entrez gene ID ['GS', 'ENSG00000258364', 'ENSG00000260628', 'MT-RNR1', 'MT-RNR2', 'MT-TC', 'MT-TF', 'SP91']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['DH5', 'ENSG00000220256', 'ENSG00000229481', 'ENSG00000244227', 'ENSG00000260158', 'ENSG00000267260']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['DH3', 'ENSG00000235704']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs mapping to duplicated target IDs in mapping table: 2\n",
"Warning: query IDs not mapped to any target IDs excluded: 34\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"34 Hugo symbols not mapped to Entrez gene ID ['AZI1', 'LOC101929676', 'AHK', 'CAC1C-AS1', 'CNTP4', 'DH2', 'DH3', 'DH5', 'DH7', 'DH8', 'DH9', 'DJB11', 'DJB3', 'DJC1', 'ENSG00000161103', 'ENSG00000162947', 'ENSG00000204044', 'ENSG00000204957', 'ENSG00000205830', 'ENSG00000222961', 'ENSG00000228318', 'ENSG00000228829', 'ENSG00000229481', 'ENSG00000231933', 'ENSG00000239636', 'ENSG00000242590', 'ENSG00000249494', 'ENSG00000252868', 'ENSG00000257434', 'ENSG00000259069', 'ENSG00000263826', 'ENSG00000272373', 'SERPI4', 'SI1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 6\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"6 Hugo symbols not mapped to Entrez gene ID ['DH9', 'ENSG00000207207', 'ENSG00000237031', 'ENSG00000237281', 'ENSG00000263272', 'ENSG00000267462']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 8\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"8 Hugo symbols not mapped to Entrez gene ID ['DH8', 'ENSG00000215923', 'ENSG00000221672', 'ENSG00000222043', 'ENSG00000225946', 'ENSG00000226145', 'ENSG00000254967', 'PLX2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n",
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['AHK', 'CHR4', 'ENSG00000221186', 'ENSG00000235837', 'ENSG00000270540']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000259241', 'MT-CO1', 'MT-ND5']\n",
"4 Hugo symbols not mapped to Entrez gene ID ['AHK', 'ENSG00000206195', 'ENSG00000225411', 'ENSG00000273312']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"LGG\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 287 fies;\t\traw maf: 531 files\n",
"select raw maf file for cohort LGG\n",
"use path ../../TCGA/mutations/data_raw/gdac.broadinstitute.org_LGG.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"STAD\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 290 fies;\t\traw maf: 396 files\n",
"select raw maf file for cohort STAD\n",
"use path ../../TCGA/mutations/data_raw/gdac.broadinstitute.org_STAD.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0/\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000214999', 'ENSG00000255641']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['MT-ND5', 'MT-ND6']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['C11orf48']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['LOC101927016', 'ENSG00000181495']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000251606']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['AGPAT9']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['AZI1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000269808']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000255622']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000268412', 'ENSG00000269175', 'KIAA1804']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['C10orf2']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['AZI1', 'ENSG00000267882']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000258027']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['LOC100996735', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['B3GNT1', 'ENSG00000212884']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000180574']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000189332']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n",
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n",
"1 Hugo symbols not mapped to Entrez gene ID ['101928757']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['101928757', 'ENSG00000180574']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CD97']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000243696', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['AZI1', 'ENSG00000180574', 'ENSG00000269175']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000258027']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000261711']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['LOC100996735', 'ENSG00000259455']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['AZI1', 'C10orf2', 'ENSG00000243501', 'ENSG00000255168', 'ENSG00000269175']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['101928757']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000250850', 'ENSG00000267976']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['CD97', 'EFTUD1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['TRAPPC2P1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['MT-CO1', 'MT-ND4L']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000250692']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['EFTUD1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['EFTUD1', 'LOC101927016', '101928503']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000180574']\n",
"1"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
" Hugo symbols not mapped to Entrez gene ID ['LOC101927016']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['HN1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000243501']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['B3GNT1', 'KIAA1045']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-CO1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000269175', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['CXXC11', 'EFTUD1', '101928503', 'ENSG00000249034', 'ENSG00000268467']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000234719']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CXXC11']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['KIAA1045']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000121388']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000269846']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000187811']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['AZI1', 'MT-ND6']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000180574']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['CD97', 'CSRP2BP', 'ENSG00000259966', 'ENSG00000269175']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000273398', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000212884']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 7\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"7 Hugo symbols not mapped to Entrez gene ID ['AIM1', 'AZI1', 'CSRP2BP', 'NAT6', '101928757', 'ENSG00000255622', 'KIAA1045']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['C10orf2', 'ENSG00000255622']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000268412', 'ENSG00000269175', 'MT-ATP6']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['APITD1', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['B3GNT1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['EFTUD1', '101928757']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ADC']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['AZI1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 5\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"5 Hugo symbols not mapped to Entrez gene ID ['ADC', 'FAM21A', 'SLC35E2', 'ENSG00000234719', 'ENSG00000255168']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000273398']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['ENSG00000244558', 'ENSG00000255182']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 4\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"4 Hugo symbols not mapped to Entrez gene ID ['CXXC11', 'ENSG00000255168', 'ENSG00000268412', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 3\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"3 Hugo symbols not mapped to Entrez gene ID ['ENSG00000258654', 'MT-CO1', 'MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['C10orf2', 'ENSG00000255641']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000173213']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CD97']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['AZI1']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000189332']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['ENSG00000272822']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['MT-ND5']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['CSRP2BP', 'ENSG00000243008']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CSRP2BP']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 2\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2 Hugo symbols not mapped to Entrez gene ID ['AGPAT9', 'FAM21A']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Warning: query IDs not mapped to any target IDs excluded: 1\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"1 Hugo symbols not mapped to Entrez gene ID ['CSRP2BP']\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"READ\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"preprocessed maf 70 fies;\t\traw maf: 123 files\n",
"select raw maf file for cohort READ\n",
"use path ../../TCGA/mutations/data_raw/gdac.broadinstitute.org_READ.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0/\n",
"Protein change columns not found in TCGA-CI-6619-01.maf.txt READ\n"
]
},
{
"ename": "KeyError",
"evalue": "\"['AAChange'] not in index\"",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-183-bb4286da1065>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 42\u001b[0m \u001b[0;32mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Protein change columns not found in\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcohort\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mfile\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstderr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 43\u001b[0m \u001b[0mdf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfillna\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m{\u001b[0m\u001b[0mprotein_change\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\"NA\"\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minplace\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 44\u001b[0;31m \u001b[0mdf\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mread_broad_maf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtcga_point\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtcga_truncating\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mprotein_change\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mprotein_change\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 45\u001b[0m \u001b[0;31m# if all Entrez gene IDs are zeroes\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 46\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"Entrez_gene_ID\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalues\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m<ipython-input-177-42df2c6b4575>\u001b[0m in \u001b[0;36mread_broad_maf\u001b[0;34m(df, point, truncating, protein_change)\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mread_broad_maf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpoint\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtruncating\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mprotein_change\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"Protein_Change\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m df = df[[\"Hugo_Symbol\",\"Entrez_Gene_Id\",\"Variant_Classification\",\n\u001b[0;32m----> 3\u001b[0;31m protein_change,'Tumor_Sample_Barcode']].copy()\n\u001b[0m\u001b[1;32m 4\u001b[0m \u001b[0;31m# 'Chromosome', u'Start_position', u'End_position']].copy()\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;34m\"-Tumor\"\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mdf\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"Tumor_Sample_Barcode\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalues\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/home/olya/miniconda2/lib/python2.7/site-packages/pandas/core/frame.pyc\u001b[0m in \u001b[0;36m__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 2680\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mSeries\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mndarray\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mIndex\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2681\u001b[0m \u001b[0;31m# either boolean or fancy integer index\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2682\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getitem_array\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2683\u001b[0m \u001b[0;32melif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mDataFrame\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2684\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getitem_frame\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/home/olya/miniconda2/lib/python2.7/site-packages/pandas/core/frame.pyc\u001b[0m in \u001b[0;36m_getitem_array\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 2724\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_take\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2725\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2726\u001b[0;31m \u001b[0mindexer\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_convert_to_indexer\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2727\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_take\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2728\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/home/olya/miniconda2/lib/python2.7/site-packages/pandas/core/indexing.pyc\u001b[0m in \u001b[0;36m_convert_to_indexer\u001b[0;34m(self, obj, axis, is_setter)\u001b[0m\n\u001b[1;32m 1325\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mmask\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0many\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1326\u001b[0m raise KeyError('{mask} not in index'\n\u001b[0;32m-> 1327\u001b[0;31m .format(mask=objarr[mask]))\n\u001b[0m\u001b[1;32m 1328\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1329\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mcom\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_values_from_object\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mKeyError\u001b[0m: \"['AAChange'] not in index\""
]
}
],
"source": [
"tcga_point = ['In_Frame_Del','In_Frame_Ins','Missense_Mutation']\n",
"tcga_truncating = ['Frame_Shift_Del','Frame_Shift_Ins','Nonsense_Mutation',\n",
" 'Splice_Site','Translation_Start_Site','Nonstop_Mutation']\n",
"\n",
"vatiant_types = set()\n",
"for cohort in cohorts: \n",
" print(cohort)\n",
" tcga = {}\n",
" \n",
" # decide which mutation file to use\n",
" proc_maf_path = \"../../TCGA/mutations/data/gdac.broadinstitute.org_\"+cohort+\".Mutation_Packager_Calls.Level_3.2016012800.0.0/\"\n",
" raw_maf_path = \"../../TCGA/mutations/data_raw/gdac.broadinstitute.org_\"+cohort+\".Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0/\"\n",
" proc_maf_files, raw_maf_files = 0, 0 \n",
" if os.path.exists(processed_maf_path):\n",
" proc_maf_files = len(os.listdir(proc_maf_path))\n",
" if os.path.exists(raw_maf_path):\n",
" raw_maf_files = len(os.listdir(raw_maf_path))\n",
" # select the one with maximal number of mutations\n",
" print(\"preprocessed maf\",proc_maf_files,\"fies;\\t\\traw maf:\",raw_maf_files,\"files\",file = sys.stderr)\n",
" if raw_maf_files > proc_maf_files:\n",
" path = raw_maf_path\n",
" print(\"select raw maf file for cohort\", cohort, file =sys.stderr )\n",
" else:\n",
" path = proc_maf_path\n",
" print(\"select processed maf file for cohort\", cohort, file =sys.stderr )\n",
" print(\"use path\",path, file = sys.stderr)\n",
" for fname in os.listdir(path):\n",
" if fname.endswith(\".maf.txt\"):\n",
" #print(sname)\n",
" df = pd.read_csv(path+fname, sep = \"\\t\")\n",
" sname = df[\"Tumor_Sample_Barcode\"].values[0]\n",
" vatiant_types = vatiant_types | set(df[\"Variant_Classification\"].values)\n",
" if \"Protein_Change\" in df.columns:\n",
" protein_change = \"Protein_Change\"\n",
" elif \"amino_acid_change_WU\" in df.columns:\n",
" protein_change = \"amino_acid_change_WU\"\n",
" elif \"AAChange\" in df.columns:\n",
" protein_change = \"AAChange\"\n",
" elif \"amino_acid_change\" in df.columns:\n",
" protein_change = \"amino_acid_change\"\n",
" else:\n",
" print(\"Protein change columns not found in\", fname, cohort,file=sys.stderr)\n",
" df.fillna(value={protein_change:\"NA\"}, inplace=True)\n",
" df = read_broad_maf(df, tcga_point, tcga_truncating, protein_change = protein_change)\n",
" # if all Entrez gene IDs are zeroes\n",
" if set(df[\"Entrez_gene_ID\"].values) == set([0]):\n",
" # remap Hugo symbols \n",
" df = hgnc2entrez_mapper(df,ncbi_symbols,ncbi_synonyms)\n",
" elif 0 in set(df[\"Entrez_gene_ID\"].values) :\n",
" # if zero in Entrez gene IDs, remove \n",
" df = df.loc[df[\"Entrez_gene_ID\"]!=0,:]\n",
" if df.shape[0] == 0:\n",
" tcga[sname] = {}\n",
" else:\n",
" # exlued point mutations with undefined postions \n",
" s = df.loc[df[\"aa_pos\"]== (\"NA\",\"NA\"),:].loc[df[\"function\"]== \"point_mutation\",:]\n",
" if s.shape[0] > 0:\n",
" print(s[[\"Hugo_Symbol\",\"Entrez_gene_ID\",\"Variant_Classification\",\n",
" \"function\",protein_change,\"aa_pos\"]],file = sys.stderr)\n",
" df = df.loc[~df.index.isin(s.index.values),:]\n",
" if s.shape[0] > 5:\n",
" print(sname, cohort,s.shape[0],\"point mutations without a position\",df.shape[0],\"remain\",file = sys.stderr)\n",
" if df.shape[0] == 0:\n",
" tcga[sname] = {}\n",
" else:\n",
" tcga[sname] = mutations2score(df, TSG_entrez,OG_entrez, hotspots, w=w)\n",
" # write table\n",
" tcga = pd.DataFrame.from_dict(tcga)\n",
" tcga.fillna(0,inplace = True)\n",
" tcga.to_csv(preprocessed_dir+\"/TCGA-\"+cohort+\".non_bin_mutations.tsv\",sep = \"\\t\")\n",
" # binarize and write\n",
" #tcga= tcga.applymap(lambda x: binarize(x))\n",
" #tcga.to_csv(preprocessed_dir+\"/TCGA-\"+cohort+\".binary_mutations.tsv\",sep = \"\\t\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"vatiant_types "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"tcga.loc[[7157,5925,5290,4893],:]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
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Datasets
Models
