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Marco Lenoir
MarcoTheBlack/
KGWAS
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a b/demo/run_magma.ipynb 

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{





  
  

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 "cells": [





  
  

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  {





  
  

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   "cell_type": "markdown",





  
  

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   "metadata": {},





  
  

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   "source": [





  
  

  7
  
    "## Run MAGMA on KGWAS Sumstats to get gene-based p-values\n",





  
  

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    "Given the local bfile where it stores the genotype data, you can run MAGMA to get gene-based p-values. Here is an example code to run it assuming you have (1) saved a trained model under `./data/model/test` (2) downloaded magma executable from [here](https://cncr.nl/research/magma/) (3) have a genotype file for your cohort"





  
  

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  {





  
  

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   "cell_type": "code",





  
  

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   "execution_count": 1,





  
  

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   "metadata": {},





  
  

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   "outputs": [





  
  

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    {





  
  

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     "name": "stdout",





  
  

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     "output_type": "stream",





  
  

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     "text": [





  
  

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      "All required data files are present.\n",





  
  

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      "--loading KG---\n",





  
  

  22
  
      "--using enformer SNP embedding--\n",





  
  

  23
  
      "--using random go embedding--\n",





  
  

  24
  
      "--using ESM gene embedding--\n",





  
  

  25
  
      "Loading example GWAS file...\n",





  
  

  26
  
      "Example file already exists locally.\n",





  
  

  27
  
      "Loading GWAS file from ./data/biochemistry_Creatinine_fastgwa_full_10000_1.fastGWA...\n",





  
  

  28
  
      "Using ldsc weight...\n",





  
  

  29
  
      "ldsc_weight mean:  0.9999999999999993\n",





  
  

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      "Annotation file already exists locally.\n",





  
  

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      "MAGMA command executed successfully.\n",





  
  

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      "Output: Welcome to MAGMA v1.10 (linux)\n",





  
  

  33
  
      "Using flags:\n",





  
  

  34
  
      "\t--bfile /dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_sample_0.1\n",





  
  

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      "\t--gene-annot ./data/gene_annotation.genes.annot\n",





  
  

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      "\t--pval ./data//model_pred/new_experiments/test_magma_format.csv N=9988\n",





  
  

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      "\t--out ./data//model_pred/new_experiments/test_magma_out\n",





  
  

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      "\n",





  
  

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      "Start time is 21:07:31, Monday 25 Nov 2024\n",





  
  

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      "\n",





  
  

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      "Loading PLINK-format data...\n",





  
  

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      "Reading file /dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_sample_0.1.fam... 48769 individuals read\n",





  
  

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      "Reading file /dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_sample_0.1.bim... 784256 SNPs read\n",





  
  

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      "Preparing file /dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_sample_0.1.bed... \n",





  
  

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      "\n",





  
  

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      "Reading SNP p-values from file ./data//model_pred/new_experiments/test_magma_format.csv... \n",





  
  

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      "\tdetected 2 variables in file\n",





  
  

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      "\tusing variable: SNP (SNP id)\n",





  
  

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      "\tusing variable: P (p-value)\n",





  
  

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      "\tread 542759 lines from file, containing valid SNP p-values for 542758 SNPs in data (100% of lines, 69.21% of SNPs in data)\n",





  
  

  51
  
      "Loading gene annotation from file ./data/gene_annotation.genes.annot... \n",





  
  

  52
  
      "\t17919 gene definitions read from file\n",





  
  

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      "\tfound 16637 genes containing valid SNPs in genotype data\n",





  
  

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      "\n",





  
  

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      "\n",





  
  

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      "Starting gene analysis... \n",





  
  

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      "\tusing model: SNPwise-mean\n",





  
  

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      "\tprocessed genes: 16632 (100%)     \n",





  
  

  752
  
      "                                                                                                                   \n",





  
  

  753
  
      "\twriting gene analysis results to file ./data//model_pred/new_experiments/test_magma_out.genes.out\n",





  
  

  754
  
      "\twriting intermediate output to file ./data//model_pred/new_experiments/test_magma_out.genes.raw\n",





  
  

  755
  
      "\n",





  
  

  756
  
      "\n",





  
  

  757
  
      "End time is 21:34:07, Monday 25 Nov 2024 (elapsed: 00:26:36)\n",





  
  

  758
  
      "\n"





  
  

  759
  
     ]





  
  

  760
  
    }





  
  

  761
  
   ],





  
  

  762
  
   "source": [





  
  

  763
  
    "import sys\n",





  
  

  764
  
    "sys.path.append('../')\n",





  
  

  765
  
    "from kgwas import KGWAS, KGWAS_Data\n",





  
  

  766
  
    "data = KGWAS_Data(data_path = './data/')\n",





  
  

  767
  
    "data.load_kg()\n",





  
  

  768
  
    "\n",





  
  

  769
  
    "data.load_external_gwas(example_file = True)\n",





  
  

  770
  
    "data.process_gwas_file()\n",





  
  

  771
  
    "data.prepare_split()\n",





  
  

  772
  
    "\n",





  
  

  773
  
    "run = KGWAS(data, device = 'cuda:7', exp_name = 'test')\n",





  
  

  774
  
    "run.load_pretrained('./data/model/test')\n",





  
  

  775
  
    "run.run_magma(path_to_magma = \"/dfs/user/kexinh/ggwas/magma\", bfile = \"/dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_sample_0.1\")"





  
  

  776
  
   ]





  
  

  777
  
  },





  
  

  778
  
  {





  
  

  779
  
   "cell_type": "markdown",





  
  

  780
  
   "metadata": {},





  
  

  781
  
   "source": [





  
  

  782
  
    "Here is an example output of the MAGMA run:"





  
  

  783
  
   ]





  
  

  784
  
  },





  
  

  785
  
  {





  
  

  786
  
   "cell_type": "code",





  
  

  787
  
   "execution_count": 1,





  
  

  788
  
   "metadata": {},





  
  

  789
  
   "outputs": [





  
  

  790
  
    {





  
  

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       "\n",





  
  

  799
  
       "    .dataframe tbody tr th {\n",





  
  

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       "        vertical-align: top;\n",





  
  

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       "    }\n",





  
  

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       "\n",





  
  

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       "    .dataframe thead th {\n",





  
  

  804
  
       "        text-align: right;\n",





  
  

  805
  
       "    }\n",





  
  

  806
  
       "</style>\n",





  
  

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       "<table border=\"1\" class=\"dataframe\">\n",





  
  

  808
  
       "  <thead>\n",





  
  

  809
  
       "    <tr style=\"text-align: right;\">\n",





  
  

  810
  
       "      <th></th>\n",





  
  

  811
  
       "      <th>GENE</th>\n",





  
  

  812
  
       "      <th>CHR</th>\n",





  
  

  813
  
       "      <th>START</th>\n",





  
  

  814
  
       "      <th>STOP</th>\n",





  
  

  815
  
       "      <th>NSNPS</th>\n",





  
  

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       "      <th>NPARAM</th>\n",





  
  

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       "    </tr>\n",





  
  

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       "    <tr>\n",





  
  

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       "      <th>1</th>\n",





  
  

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       "      <td>26155</td>\n",





  
  

  838
  
       "      <td>1</td>\n",





  
  

  839
  
       "      <td>879583</td>\n",





  
  

  840
  
       "      <td>894679</td>\n",





  
  

  841
  
       "      <td>9</td>\n",





  
  

  842
  
       "      <td>4</td>\n",





  
  

  843
  
       "      <td>9988</td>\n",





  
  

  844
  
       "      <td>0.36490</td>\n",





  
  

  845
  
       "      <td>0.357590</td>\n",





  
  

  846
  
       "    </tr>\n",





  
  

  847
  
       "    <tr>\n",





  
  

  848
  
       "      <th>2</th>\n",





  
  

  849
  
       "      <td>339451</td>\n",





  
  

  850
  
       "      <td>1</td>\n",





  
  

  851
  
       "      <td>895967</td>\n",





  
  

  852
  
       "      <td>901099</td>\n",





  
  

  853
  
       "      <td>1</td>\n",





  
  

  854
  
       "      <td>1</td>\n",





  
  

  855
  
       "      <td>9988</td>\n",





  
  

  856
  
       "      <td>1.40540</td>\n",





  
  

  857
  
       "      <td>0.079955</td>\n",





  
  

  858
  
       "    </tr>\n",





  
  

  859
  
       "    <tr>\n",





  
  

  860
  
       "      <th>3</th>\n",





  
  

  861
  
       "      <td>84069</td>\n",





  
  

  862
  
       "      <td>1</td>\n",





  
  

  863
  
       "      <td>901872</td>\n",





  
  

  864
  
       "      <td>910488</td>\n",





  
  

  865
  
       "      <td>3</td>\n",





  
  

  866
  
       "      <td>2</td>\n",





  
  

  867
  
       "      <td>9988</td>\n",





  
  

  868
  
       "      <td>1.56410</td>\n",





  
  

  869
  
       "      <td>0.058896</td>\n",





  
  

  870
  
       "    </tr>\n",





  
  

  871
  
       "    <tr>\n",





  
  

  872
  
       "      <th>4</th>\n",





  
  

  873
  
       "      <td>84808</td>\n",





  
  

  874
  
       "      <td>1</td>\n",





  
  

  875
  
       "      <td>910579</td>\n",





  
  

  876
  
       "      <td>917473</td>\n",





  
  

  877
  
       "      <td>2</td>\n",





  
  

  878
  
       "      <td>1</td>\n",





  
  

  879
  
       "      <td>9988</td>\n",





  
  

  880
  
       "      <td>1.25460</td>\n",





  
  

  881
  
       "      <td>0.104820</td>\n",





  
  

  882
  
       "    </tr>\n",





  
  

  883
  
       "    <tr>\n",





  
  

  884
  
       "      <th>...</th>\n",





  
  

  885
  
       "      <td>...</td>\n",





  
  

  886
  
       "      <td>...</td>\n",





  
  

  887
  
       "      <td>...</td>\n",





  
  

  888
  
       "      <td>...</td>\n",





  
  

  889
  
       "      <td>...</td>\n",





  
  

  890
  
       "      <td>...</td>\n",





  
  

  891
  
       "      <td>...</td>\n",





  
  

  892
  
       "      <td>...</td>\n",





  
  

  893
  
       "      <td>...</td>\n",





  
  

  894
  
       "    </tr>\n",





  
  

  895
  
       "    <tr>\n",





  
  

  896
  
       "      <th>16632</th>\n",





  
  

  897
  
       "      <td>23542</td>\n",





  
  

  898
  
       "      <td>22</td>\n",





  
  

  899
  
       "      <td>51039131</td>\n",





  
  

  900
  
       "      <td>51049979</td>\n",





  
  

  901
  
       "      <td>3</td>\n",





  
  

  902
  
       "      <td>2</td>\n",





  
  

  903
  
       "      <td>9988</td>\n",





  
  

  904
  
       "      <td>1.15830</td>\n",





  
  

  905
  
       "      <td>0.123360</td>\n",





  
  

  906
  
       "    </tr>\n",





  
  

  907
  
       "    <tr>\n",





  
  

  908
  
       "      <th>16633</th>\n",





  
  

  909
  
       "      <td>410</td>\n",





  
  

  910
  
       "      <td>22</td>\n",





  
  

  911
  
       "      <td>51061182</td>\n",





  
  

  912
  
       "      <td>51066601</td>\n",





  
  

  913
  
       "      <td>9</td>\n",





  
  

  914
  
       "      <td>5</td>\n",





  
  

  915
  
       "      <td>9988</td>\n",





  
  

  916
  
       "      <td>-0.65834</td>\n",





  
  

  917
  
       "      <td>0.744840</td>\n",





  
  

  918
  
       "    </tr>\n",





  
  

  919
  
       "    <tr>\n",





  
  

  920
  
       "      <th>16634</th>\n",





  
  

  921
  
       "      <td>85358</td>\n",





  
  

  922
  
       "      <td>22</td>\n",





  
  

  923
  
       "      <td>51113070</td>\n",





  
  

  924
  
       "      <td>51171640</td>\n",





  
  

  925
  
       "      <td>41</td>\n",





  
  

  926
  
       "      <td>15</td>\n",





  
  

  927
  
       "      <td>9988</td>\n",





  
  

  928
  
       "      <td>-1.18500</td>\n",





  
  

  929
  
       "      <td>0.881990</td>\n",





  
  

  930
  
       "    </tr>\n",





  
  

  931
  
       "    <tr>\n",





  
  

  932
  
       "      <th>16635</th>\n",





  
  

  933
  
       "      <td>101928892</td>\n",





  
  

  934
  
       "      <td>22</td>\n",





  
  

  935
  
       "      <td>51123086</td>\n",





  
  

  936
  
       "      <td>51125473</td>\n",





  
  

  937
  
       "      <td>2</td>\n",





  
  

  938
  
       "      <td>1</td>\n",





  
  

  939
  
       "      <td>9988</td>\n",





  
  

  940
  
       "      <td>-0.14590</td>\n",





  
  

  941
  
       "      <td>0.558000</td>\n",





  
  

  942
  
       "    </tr>\n",





  
  

  943
  
       "    <tr>\n",





  
  

  944
  
       "      <th>16636</th>\n",





  
  

  945
  
       "      <td>49</td>\n",





  
  

  946
  
       "      <td>22</td>\n",





  
  

  947
  
       "      <td>51176652</td>\n",





  
  

  948
  
       "      <td>51183727</td>\n",





  
  

  949
  
       "      <td>1</td>\n",





  
  

  950
  
       "      <td>1</td>\n",





  
  

  951
  
       "      <td>9988</td>\n",





  
  

  952
  
       "      <td>-0.42425</td>\n",





  
  

  953
  
       "      <td>0.664310</td>\n",





  
  

  954
  
       "    </tr>\n",





  
  

  955
  
       "  </tbody>\n",





  
  

  956
  
       "</table>\n",





  
  

  957
  
       "<p>16637 rows × 9 columns</p>\n",





  
  

  958
  
       "</div>"





  
  

  959
  
      ],





  
  

  960
  
      "text/plain": [





  
  

  961
  
       "            GENE  CHR     START      STOP  NSNPS  NPARAM     N    ZSTAT  \\\n",





  
  

  962
  
       "0         148398    1    859993    879961      6       4  9988 -1.10670   \n",





  
  

  963
  
       "1          26155    1    879583    894679      9       4  9988  0.36490   \n",





  
  

  964
  
       "2         339451    1    895967    901099      1       1  9988  1.40540   \n",





  
  

  965
  
       "3          84069    1    901872    910488      3       2  9988  1.56410   \n",





  
  

  966
  
       "4          84808    1    910579    917473      2       1  9988  1.25460   \n",





  
  

  967
  
       "...          ...  ...       ...       ...    ...     ...   ...      ...   \n",





  
  

  968
  
       "16632      23542   22  51039131  51049979      3       2  9988  1.15830   \n",





  
  

  969
  
       "16633        410   22  51061182  51066601      9       5  9988 -0.65834   \n",





  
  

  970
  
       "16634      85358   22  51113070  51171640     41      15  9988 -1.18500   \n",





  
  

  971
  
       "16635  101928892   22  51123086  51125473      2       1  9988 -0.14590   \n",





  
  

  972
  
       "16636         49   22  51176652  51183727      1       1  9988 -0.42425   \n",





  
  

  973
  
       "\n",





  
  

  974
  
       "              P  \n",





  
  

  975
  
       "0      0.865800  \n",





  
  

  976
  
       "1      0.357590  \n",





  
  

  977
  
       "2      0.079955  \n",





  
  

  978
  
       "3      0.058896  \n",





  
  

  979
  
       "4      0.104820  \n",





  
  

  980
  
       "...         ...  \n",





  
  

  981
  
       "16632  0.123360  \n",





  
  

  982
  
       "16633  0.744840  \n",





  
  

  983
  
       "16634  0.881990  \n",





  
  

  984
  
       "16635  0.558000  \n",





  
  

  985
  
       "16636  0.664310  \n",





  
  

  986
  
       "\n",





  
  

  987
  
       "[16637 rows x 9 columns]"





  
  

  988
  
      ]





  
  

  989
  
     },





  
  

  990
  
     "execution_count": 1,





  
  

  991
  
     "metadata": {},





  
  

  992
  
     "output_type": "execute_result"





  
  

  993
  
    }





  
  

  994
  
   ],





  
  

  995
  
   "source": [





  
  

  996
  
    "import pandas as pd\n",





  
  

  997
  
    "pd.read_csv('./data/model_pred/new_experiments/test_magma_out.genes.out', sep = '\\s+')"





  
  

  998
  
   ]





  
  

  999
  
  },





  
  

  1000
  
  {





  
  

  1001
  
   "cell_type": "markdown",





  
  

  1002
  
   "metadata": {},





  
  

  1003
  
   "source": [





  
  

  1004
  
    "To know which gene this gene id maps to, you can use the following file:"





  
  

  1005
  
   ]





  
  

  1006
  
  },





  
  

  1007
  
  {





  
  

  1008
  
   "cell_type": "code",





  
  

  1009
  
   "execution_count": 14,





  
  

  1010
  
   "metadata": {},





  
  

  1011
  
   "outputs": [





  
  

  1012
  
    {





  
  

  1013
  
     "data": {





  
  

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       "        vertical-align: middle;\n",





  
  

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       "\n",





  
  

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       "        vertical-align: top;\n",





  
  

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       "\n",





  
  

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       "    .dataframe thead th {\n",





  
  

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       "        text-align: right;\n",





  
  

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       "    }\n",





  
  

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       "</style>\n",





  
  

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  1030
  
       "  <thead>\n",





  
  

  1031
  
       "    <tr style=\"text-align: right;\">\n",





  
  

  1032
  
       "      <th></th>\n",





  
  

  1033
  
       "      <th>0</th>\n",





  
  

  1034
  
       "      <th>1</th>\n",





  
  

  1035
  
       "      <th>2</th>\n",





  
  

  1036
  
       "      <th>3</th>\n",





  
  

  1037
  
       "      <th>4</th>\n",





  
  

  1038
  
       "      <th>5</th>\n",





  
  

  1039
  
       "    </tr>\n",





  
  

  1040
  
       "  </thead>\n",





  
  

  1041
  
       "  <tbody>\n",





  
  

  1042
  
       "    <tr>\n",





  
  

  1043
  
       "      <th>0</th>\n",





  
  

  1044
  
       "      <td>79501</td>\n",





  
  

  1045
  
       "      <td>1</td>\n",





  
  

  1046
  
       "      <td>69091</td>\n",





  
  

  1047
  
       "      <td>70008</td>\n",





  
  

  1048
  
       "      <td>+</td>\n",





  
  

  1049
  
       "      <td>OR4F5</td>\n",





  
  

  1050
  
       "    </tr>\n",





  
  

  1051
  
       "    <tr>\n",





  
  

  1052
  
       "      <th>1</th>\n",





  
  

  1053
  
       "      <td>100996442</td>\n",





  
  

  1054
  
       "      <td>1</td>\n",





  
  

  1055
  
       "      <td>142447</td>\n",





  
  

  1056
  
       "      <td>174392</td>\n",





  
  

  1057
  
       "      <td>-</td>\n",





  
  

  1058
  
       "      <td>LOC100996442</td>\n",





  
  

  1059
  
       "    </tr>\n",





  
  

  1060
  
       "    <tr>\n",





  
  

  1061
  
       "      <th>2</th>\n",





  
  

  1062
  
       "      <td>729759</td>\n",





  
  

  1063
  
       "      <td>1</td>\n",





  
  

  1064
  
       "      <td>367659</td>\n",





  
  

  1065
  
       "      <td>368597</td>\n",





  
  

  1066
  
       "      <td>+</td>\n",





  
  

  1067
  
       "      <td>OR4F29</td>\n",





  
  

  1068
  
       "    </tr>\n",





  
  

  1069
  
       "    <tr>\n",





  
  

  1070
  
       "      <th>3</th>\n",





  
  

  1071
  
       "      <td>81399</td>\n",





  
  

  1072
  
       "      <td>1</td>\n",





  
  

  1073
  
       "      <td>621096</td>\n",





  
  

  1074
  
       "      <td>622034</td>\n",





  
  

  1075
  
       "      <td>-</td>\n",





  
  

  1076
  
       "      <td>OR4F16</td>\n",





  
  

  1077
  
       "    </tr>\n",





  
  

  1078
  
       "    <tr>\n",





  
  

  1079
  
       "      <th>4</th>\n",





  
  

  1080
  
       "      <td>148398</td>\n",





  
  

  1081
  
       "      <td>1</td>\n",





  
  

  1082
  
       "      <td>859993</td>\n",





  
  

  1083
  
       "      <td>879961</td>\n",





  
  

  1084
  
       "      <td>+</td>\n",





  
  

  1085
  
       "      <td>SAMD11</td>\n",





  
  

  1086
  
       "    </tr>\n",





  
  

  1087
  
       "    <tr>\n",





  
  

  1088
  
       "      <th>...</th>\n",





  
  

  1089
  
       "      <td>...</td>\n",





  
  

  1090
  
       "      <td>...</td>\n",





  
  

  1091
  
       "      <td>...</td>\n",





  
  

  1092
  
       "      <td>...</td>\n",





  
  

  1093
  
       "      <td>...</td>\n",





  
  

  1094
  
       "      <td>...</td>\n",





  
  

  1095
  
       "    </tr>\n",





  
  

  1096
  
       "    <tr>\n",





  
  

  1097
  
       "      <th>19422</th>\n",





  
  

  1098
  
       "      <td>442867</td>\n",





  
  

  1099
  
       "      <td>Y</td>\n",





  
  

  1100
  
       "      <td>26764151</td>\n",





  
  

  1101
  
       "      <td>26785354</td>\n",





  
  

  1102
  
       "      <td>+</td>\n",





  
  

  1103
  
       "      <td>BPY2B</td>\n",





  
  

  1104
  
       "    </tr>\n",





  
  

  1105
  
       "    <tr>\n",





  
  

  1106
  
       "      <th>19423</th>\n",





  
  

  1107
  
       "      <td>57054</td>\n",





  
  

  1108
  
       "      <td>Y</td>\n",





  
  

  1109
  
       "      <td>26909216</td>\n",





  
  

  1110
  
       "      <td>26959639</td>\n",





  
  

  1111
  
       "      <td>-</td>\n",





  
  

  1112
  
       "      <td>DAZ3</td>\n",





  
  

  1113
  
       "    </tr>\n",





  
  

  1114
  
       "    <tr>\n",





  
  

  1115
  
       "      <th>19424</th>\n",





  
  

  1116
  
       "      <td>57135</td>\n",





  
  

  1117
  
       "      <td>Y</td>\n",





  
  

  1118
  
       "      <td>26979967</td>\n",





  
  

  1119
  
       "      <td>27053187</td>\n",





  
  

  1120
  
       "      <td>+</td>\n",





  
  

  1121
  
       "      <td>DAZ4</td>\n",





  
  

  1122
  
       "    </tr>\n",





  
  

  1123
  
       "    <tr>\n",





  
  

  1124
  
       "      <th>19425</th>\n",





  
  

  1125
  
       "      <td>442868</td>\n",





  
  

  1126
  
       "      <td>Y</td>\n",





  
  

  1127
  
       "      <td>27177048</td>\n",





  
  

  1128
  
       "      <td>27198251</td>\n",





  
  

  1129
  
       "      <td>-</td>\n",





  
  

  1130
  
       "      <td>BPY2C</td>\n",





  
  

  1131
  
       "    </tr>\n",





  
  

  1132
  
       "    <tr>\n",





  
  

  1133
  
       "      <th>19426</th>\n",





  
  

  1134
  
       "      <td>9085</td>\n",





  
  

  1135
  
       "      <td>Y</td>\n",





  
  

  1136
  
       "      <td>27768264</td>\n",





  
  

  1137
  
       "      <td>27771049</td>\n",





  
  

  1138
  
       "      <td>+</td>\n",





  
  

  1139
  
       "      <td>CDY1</td>\n",





  
  

  1140
  
       "    </tr>\n",





  
  

  1141
  
       "  </tbody>\n",





  
  

  1142
  
       "</table>\n",





  
  

  1143
  
       "<p>19427 rows × 6 columns</p>\n",





  
  

  1144
  
       "</div>"





  
  

  1145
  
      ],





  
  

  1146
  
      "text/plain": [





  
  

  1147
  
       "               0  1         2         3  4             5\n",





  
  

  1148
  
       "0          79501  1     69091     70008  +         OR4F5\n",





  
  

  1149
  
       "1      100996442  1    142447    174392  -  LOC100996442\n",





  
  

  1150
  
       "2         729759  1    367659    368597  +        OR4F29\n",





  
  

  1151
  
       "3          81399  1    621096    622034  -        OR4F16\n",





  
  

  1152
  
       "4         148398  1    859993    879961  +        SAMD11\n",





  
  

  1153
  
       "...          ... ..       ...       ... ..           ...\n",





  
  

  1154
  
       "19422     442867  Y  26764151  26785354  +         BPY2B\n",





  
  

  1155
  
       "19423      57054  Y  26909216  26959639  -          DAZ3\n",





  
  

  1156
  
       "19424      57135  Y  26979967  27053187  +          DAZ4\n",





  
  

  1157
  
       "19425     442868  Y  27177048  27198251  -         BPY2C\n",





  
  

  1158
  
       "19426       9085  Y  27768264  27771049  +          CDY1\n",





  
  

  1159
  
       "\n",





  
  

  1160
  
       "[19427 rows x 6 columns]"





  
  

  1161
  
      ]





  
  

  1162
  
     },





  
  

  1163
  
     "execution_count": 14,





  
  

  1164
  
     "metadata": {},





  
  

  1165
  
     "output_type": "execute_result"





  
  

  1166
  
    }





  
  

  1167
  
   ],





  
  

  1168
  
   "source": [





  
  

  1169
  
    "pd.read_csv('./data/misc_data/NCBI37.3.gene.loc', sep = '\\t', header = None)"





  
  

  1170
  
   ]





  
  

  1171
  
  },





  
  

  1172
  
  {





  
  

  1173
  
   "cell_type": "code",





  
  

  1174
  
   "execution_count": null,





  
  

  1175
  
   "metadata": {},





  
  

  1176
  
   "outputs": [],





  
  

  1177
  
   "source": []





  
  

  1178
  
  }





  
  

  1179
  
 ],





  
  

  1180
  
 "metadata": {





  
  

  1181
  
  "kernelspec": {





  
  

  1182
  
   "display_name": "a100_env",





  
  

  1183
  
   "language": "python",





  
  

  1184
  
   "name": "python3"





  
  

  1185
  
  },





  
  

  1186
  
  "language_info": {





  
  

  1187
  
   "codemirror_mode": {





  
  

  1188
  
    "name": "ipython",





  
  

  1189
  
    "version": 3





  
  

  1190
  
   },





  
  

  1191
  
   "file_extension": ".py",





  
  

  1192
  
   "mimetype": "text/x-python",





  
  

  1193
  
   "name": "python",





  
  

  1194
  
   "nbconvert_exporter": "python",





  
  

  1195
  
   "pygments_lexer": "ipython3",





  
  

  1196
  
   "version": "3.8.0"





  
  

  1197
  
  }





  
  

  1198
  
 },





  
  

  1199
  
 "nbformat": 4,





  
  

  1200
  
 "nbformat_minor": 2





  
  

  1201
  
}