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/ipynb/genome classifier.ipynb
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+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## basic classifier for Dna2Vec represenation\n",
+ "\n",
+ "Basic bacterial genome classification using Dna2Vec representation"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "%load_ext autoreload\n",
+ "%autoreload 2"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 37,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from faigen.genomic import sequence "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 38,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import sys\n",
+ "sys.path.append(\"..\")\n",
+ "from faigen.data import sequence \n",
+ "# from genomic import sequence\n",
+ "from faigen.data.sequence import regex_filter, count_filter, Dna2VecDataBunch\n",
+ "from functools import partial\n",
+ "import pandas as pd\n",
+ "import numpy as np\n",
+ "from sklearn.decomposition import PCA\n",
+ "from sklearn import manifold,neighbors\n",
+ "from scipy.cluster.hierarchy import dendrogram, linkage \n",
+ "from matplotlib import pyplot as plt\n",
+ "import seaborn as sns; sns.set(color_codes=True)\n",
+ "import plotly.plotly as py\n",
+ "import plotly.graph_objs as go\n",
+ "from fastai import *\n",
+ "from fastai.data_block import *\n",
+ "from fastai.basic_train import *\n",
+ "from fastai.layers import *\n",
+ "from fastai.metrics import *\n",
+ "import torch.nn as nn\n",
+ "import torch.nn.functional as F"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Load Data"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from gensim.models import Word2Vec\n",
+ "# word_vectors = Word2Vec.load_word2vec_format('/data/genomes/embeddings/dna2vec-20190612-1611-k10to10-100d-10c-4870Mbp-sliding-kPR.w2v') \n",
+ "\n",
+ "word_vectors = Word2Vec.load_word2vec_format('/data/genomes/embeddings/dna2vec-20190611-1940-k8to8-100d-10c-4870Mbp-sliding-LmP.w2v') \n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\n",
+ " <class 'genomic.sequence.GSFileProcessor'>\n",
+ "CPU times: user 792 ms, sys: 28 ms, total: 820 ms\n",
+ "Wall time: 820 ms\n",
+ "\n",
+ " <class 'genomic.sequence.GSTokenizeProcessor'>\n",
+ "CPU times: user 4.76 s, sys: 176 ms, total: 4.93 s\n",
+ "Wall time: 4.93 s\n",
+ "\n",
+ " <class 'genomic.sequence.Dna2VecProcessor'>\n",
+ "CPU times: user 3min 49s, sys: 166 ms, total: 3min 50s\n",
+ "Wall time: 3min 50s\n"
+ ]
+ }
+ ],
+ "source": [
+ "filters=[partial(regex_filter, rx=\"Streptomyces|Bacillus|Vibrio|Streptococcus|Rhizobium|Staphylococcus\"),partial(regex_filter, rx=\"plasmid\", keep=False)]\n",
+ "items = sequence.Dna2VecList.from_folder(\"/data/genomes/GenSeq_fastas/train\",filters=filters,agg=partial(np.mean, axis=0),n_cpus=7,emb=word_vectors)\n",
+ "processors = [\n",
+ " sequence.GSFileProcessor(),\n",
+ " sequence.GSTokenizeProcessor(tokenizer=sequence.GSTokenizer(ngram=10, skip=0, n_cpus=7)),\n",
+ " sequence.Dna2VecProcessor(emb=word_vectors)]\n",
+ "for p in processors:\n",
+ " print(\"\\n\", type(p))\n",
+ " %time p.process(items)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 67,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "bunch.sanity_check()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 39,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "../faigen/data/sequence.py:362: FutureWarning:\n",
+ "\n",
+ "set_value is deprecated and will be removed in a future release. Please use .at[] or .iat[] accessors instead\n",
+ "\n"
+ ]
+ }
+ ],
+ "source": [
+ "DB=\"/data/genomes/GenSeq_fastas\"\n",
+ "# DB='/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes'\n",
+ "\n",
+ "filters=[partial(regex_filter, rx=\"Bacillus\",keep=False),partial(regex_filter, rx=\"plasmid?\\s\", keep=False)] \n",
+ "# partial(count_filter,num_fastas=(1,1), keep=1)]\n",
+ "\n",
+ "bunch = Dna2VecDataBunch.from_folder(DB,\n",
+ " filters=filters,\n",
+ " labeler=lambda x: x.split()[1],\n",
+ " emb=word_vectors,ngram=8,skip=0,\n",
+ " n_cpus=7,agg=partial(np.mean, axis=0), one_hot=True,bs=5)\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "scrolled": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
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+ " -0.1813, 0.0265, 0.0027, -0.2820]]),\n",
+ " tensor([[0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1., 0., 0.],\n",
+ " [0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 1.],\n",
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+ " [0., 0., 0., 0., 0., 0., 0., 0., 0., 1., 0., 0., 0., 0., 0., 0., 0.]]))"
+ ]
+ },
+ "execution_count": 6,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "bunch.one_batch()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "\n",
+ "class GenomeClassifier(nn.Module):\n",
+ " def __init__(self):\n",
+ " super(GenomeClassifier, self).__init__()\n",
+ " self.l1 = nn.Linear(100, 100)\n",
+ " self.linear_classifier = nn.Linear(100, bunch.train_dl.y.c)\n",
+ "\n",
+ " def forward(self, x):\n",
+ " x = F.relu(self.l1(x))\n",
+ " x = self.linear_classifier(x)\n",
+ " return x"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "class BactClassifier(SequentialEx):\n",
+ " pass"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 19,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "layers=[nn.Linear(100,100),nn.ReLU(),nn.Linear(100,17)]"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 20,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "bc = SequentialEx(*layers)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 21,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "SequentialEx(\n",
+ " (layers): ModuleList(\n",
+ " (0): Linear(in_features=100, out_features=100, bias=True)\n",
+ " (1): ReLU()\n",
+ " (2): Linear(in_features=100, out_features=17, bias=True)\n",
+ " )\n",
+ ")"
+ ]
+ },
+ "execution_count": 21,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "bc"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 25,
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [],
+ "source": [
+ "learn = Learner(bunch, bc)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 26,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "LR Finder is complete, type {learner_name}.recorder.plot() to see the graph.\n"
+ ]
+ }
+ ],
+ "source": [
+ "learn.lr_find()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 27,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "image/png": 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XExgYSHx8PGlpaQCkpaURHx/f6mEwgIqKCkwmEwC7d+/m1KlTTXM2QgjhCGm7cnDRqJkwNMLRUZxKq89YXnjhBebPn4+bmxtvvfUWAN9//z0JCQmtev7SpUtZuHAh7733Hj4+Pk1nOvPmzWP+/PkkJCRw4MABFixYgMFgQFEUNmzYwKuvvsrYsWPJyMjg1VdfRa1W4+/vz/vvv4+Hh0cb3rIQQrRfcUUtu48VMzkxEl8vWSr/cipFUdo86WA0GgFwdXW1WiBbkjmWljpibslsPx0xt70y/31DJvtO6Hn9l6PbXSzO+nVu6xxLq4fCzpw5Q2lpKQA1NTW89dZbfPDBB03DU0II0VVcOluZMDRCzlauotXF8uyzz1JVVQXA8uXL2b9/P4cPH77qBx2FEKIzS9uVg0ajYtrIHo6O4pRaPcdSUFBA7969URSFzZs3k5aWhru7O5MmTbJlPiGEcCoyt3JjrS4WNzc3DAYDZ8+eJSwsjICAAEwmEw0NDbbMJ4QQTkFRFPaf1PP5trNytnIDrS6W5ORkHnroIWpqapgzZw4AmZmZN/3pdyGE6GjOFFzg31tOc7awishgLx69M17OVq6j1cXy4osvsnPnTlxcXBg1ahQAKpWKRYsW2SycEEI4mq6shj+uOoR3d1f+a1octyVoUatVjo7l1G5qTZQxY8ZQWFhIeno6oaGhrf4MixBCdFSn8y9gURReeGAo2kC5Q2RrtLpY9Ho9CxYs4PDhw/j5+VFZWcmQIUN48803CQ0NtWVGIYRwmJyiajy6aQgN8HR0lA6j1ZcbL126lLi4OPbt28fOnTvZt28fcXFxLFmyxJb5hBDCoXKLqogO9UatkuGv1mp1sRw8eJDf/va3eHpebG1PT09eeOEF0tPTbRZOCCEcyWS2kKevITqs8yxpbw+tLhZfX1/Onj3b7LFz587h4+Nj9VBCCOEMCktrMJktUiw3qdVzLI899hgPP/ww9957L+Hh4RQWFrJmzRqefvppW+YTQgiHyS26uH5XdKgUy81odbHcf//9REVFkZaWRlZWFiEhIbz++uscPHjQlvmEEMJhcoqrcXeTifubdVOXG48ePZrRo0c3/b2xsZF58+bJWYsQolM6X1RND5m4v2mtnmO5lnasui+EEE7LbLGQpzfQU+ZXblq7i0UlTS6E6IR0pbU0mmTivi1uOBS2e/fua267dKMvIYTobHJk4r7NblgsL7300nW3a7Vaq4URQghnkVtcTTdXDWEycX/TblgsW7dutUcOIYRwKrlF1fQI9ZIFJ9ug3XMsQgjR2VgsCuf11TK/0kZSLEIIcQVdWQ2NRovMr7SRFIsQQlwht/jixL1catw2UixCCHGFnKJq3FzVcv+VNpJiEUKIK+QWVdMjxFsm7ttIikUIIS5jtljILaqWYbB2kGIRQojL5OtraDRZ6B0htwRpKykWIYS4zDldFQAx4b4OTtJxSbEIIcRlzhVcwNvTlSBfd0dH6bCkWIQQ4jLndFXEhPvKArvtIMUihBA/qak3oiurpXe4zK+0hxSLEEL8JPun+RUplvaRYhFCiJ+cK6hCBfTSSrG0hxSLEEL85JyuivCg7nh0u6m7tosrSLEIIQQXb7N+rrBKhsGsQIpFCCEAfWUdhjqjFIsVSLEIIboEk9mCyWy55vZzBfLBSGuRYhFCdHqKovDW5xn8YdUhFEW56j7nCqvo5qYhPEhWNG4vKRYhhNNqNJr54KvjrNqUhdly7bONG9l1rIhj2eVk66rIOl951X3OFl6gV5isaGwNUixCCKfU0GjmL59nsDezmK2HCnh3zTGMJvM196+qbeTvaZls3pfb7PHq2kb+vfUMMeE+eHm48t2BvBbPbTSaydMb6C3DYFZht2LJzs4mNTWVpKQkUlNTycnJabHPzp07mTlzJgMHDmT58uXNtpWVlfGLX/yC6dOnM3XqVJYuXYrJZLJTeiGEPdU1mPjzZ4c5eb6Cecn9efD2fhw+U8qfPztCXUPLf/en8ytZtmI/Px4r4i//PszGvf8pl39vPUNdg4mHp8Uxfkg4h0+XUlJZ1+z554sNmC0KMTJxbxV2K5YlS5Ywe/Zsvv32W2bPns3ixYtb7BMVFcUrr7zCo48+2mLb+++/T0xMDOvXr2f9+vUcP36cTZs22SO6EMKO6hpM/PdnhzlTUMXjMwYwemAYk4ZHMm96f07lXeD1f6bzw+ECMnPKKa2s45u951n+STquGjX/76FExg6JYPX3Z1mz/RyZOeXsOlbEtFE9iAj2YsLQCFQqFVsP5Td7zR0ZhYB84t5a7PIpoLKyMjIzM1mxYgUAycnJvPzyy5SXlxMQENC0X3R0NABbtmyhsbGx2TFUKhU1NTVYLBYaGxsxGo2EhobaI74Qwo62HsrnbEEVv757IMNjQ5oeHz0gDI9uLny4/jj/+Car2XOGxwbzX9Pi8XR3YfjAcFSKhbRdOWzarybE34Pk0T0BCPBxJzEumO1HdKSM6YW7mwtbD+WzI0PHtFE98PXqZs+32mnZpVh0Oh2hoaFoNBoANBoNISEh6HS6ZsVyPb/61a946qmnGDNmDHV1dTz44IMMHz7clrGFEA6QmVNBZLBXs1K5ZEifIN5+ehwV1Q3oK+soqazDs5sLw2ODm1Yj1qhVPDQ1Dnc3F7YczOfnSbG4uWqajjE5MYp9J/TsOlaENsCTf353msExgdwzLsZu77Gz6zDrFnzzzTfExsbyj3/8g5qaGubNm8c333zD1KlTW32MwEAvGyaE4OCOeSvTjphbMtuPPXMbTWbOFlxg6uie133d0FCIu85xQkJ8eGrWMB69KwFPd9dm24KCvOi77SybDuRTV28kIsSLFx8Z2WI/e+uo3x9XY5di0Wq1FBcXYzab0Wg0mM1m9Ho9Wq221cdYtWoVr732Gmq1Gm9vbyZOnMjevXtvqljKygxYLFe/hr29goO9KSmptsmxbakj5pbM9mPv3FnnK2g0WYgO7t7m170yc011fYt9fjYknA/XZ9Ld3YVf3zWAmur6q+5nL876/aFWq9r0C7ldJu8DAwOJj48nLS0NgLS0NOLj41s9DAYQGRnJ9u3bAWhsbGT37t307dvXJnmFEI6Rdb4SFdCvh59NX2dEXAgThkXw1D2DCPH3tOlrdUV2GwpbunQpCxcu5L333sPHx6fpcuJ58+Yxf/58EhISOHDgAAsWLMBgMKAoChs2bODVV19l7NixvPjiiyxZsoTp06djNpsZOXIk999/v73iC+H0zhZe4IKhEbNFwWyx4OZy8VPkIX4edv/QX12DieWfHCLAx505U/oR4NO62/yePF9BVKgX3W08LOWiUTN3SqxNX6MrUynXWt+gE5KhsJY6Ym7J3NLODB0ffX3iqttcXdRoAz2JCPIiMrg7EcHdiQrxxt/7xldAtTX3yo0n2JGhw9VFjUat4r4JfRg/OPy6t/s1msz8+s87mDgsglmT2j4aId8f1tPWobAOM3kvhLg6XVkNq77LIq6HH7Mm9UWtVqFRq6hvNFNQUkNhaQ35JQZOnq9g9/EiAFTAXWN7kXxrT6vf2/3w6VK2H9Fxx6hoxg0J5x8bT/LxN1nsPV7M2MFaBvYOxMfTrcXzzhRUYTJbiIv2t2oeYX9SLEI4gKIoGOqMlFc10GA00yfCt03DVUaTmb+uPY6bi4Z50we0OAu58k6ItfVGCkpr+P5QAV/uyCa/pIZH7oinm5sGk9nCvhPFfJ9egFqlIsjXg+hwX/w8XRjWLxgXzY2nZKtqG1m58QSRwV6kjOmFq4ua52YNYfuRQr7ckc3/pp1ABfTUejN5eBSjB4Y1PfdkbgUqFfSLtO38irA9KRYh7KiuwcT7645z8nwFRtN/FlXspfXhoamx9Ai9+iWnDUYzhaU1VNc20jvcFy+Pi3MQ/956hvwSA7+5b1CrhrY83V3pG+lHnwhfokK9+Pz7sxSX1zJqQBhbDuZTVlVPeFB3vDxcOZVXwd7MIiwKhPh5kDK2FyPjQ69ZgIqi8H/fZFHbYOLZWUNxdblYRCqVivFDIhg7OJzzxdUcPVvG/pN6/ndDJmGBnk3ll3W+gp5h3ni6y4+ljk7+DwphJ41GM299nsHp/AtMGBZBiJ8HAT7dqKk3seaHs/x+5QEmJ0Yyfkg4RWW15JUYyNcbyCupQV9Ry6XZ0Eu/8UcGe7EjQ0fSLVEMigm6qSwqlYppI6OJCOrOB18d57Pvz9An0pc5U/oxKCawaXjMz7872/bnsnb7OT5cn8nXu3O5a2xvhvULajaEZjRZ2LA7h4OnSrjvZzFEhbQcl1erVPQM86FnmA+Thkfx//6+lxVfn2DxwyMwWxTOFlYxZURUW7+8wolIsQhxDVW1jRSW1BDs54G/TzfUrZyLyNcbWLP9HPE9/Rk3OJxurhqMJgvvrT3GqbxK5s3oz6j+Yc2eMzw2mM+3nWXT/jw27b+4+q4KCPbzIDLEi5HxIUQGe9Hdw5Ws8xVk5lbw49Eieml9uGd82z8xPigmiGX/dQtVtVe/c6Kri5ohfYIYFBPIgZN6vtyRzbtfHqVHqBd3je3N4JhAjpwp49Otp9FX1JEYF0LSLT1u+Lqe7i7MnRLLW19ksGF3Ln0ifTFbFJlf6STkqjArcdarOm6kI+a2R2azxcIr/zhIbvHF13HRqAn2c2dAzwBuTQgjOtS7xaS3oijsyNDxyXengIu/xXt5uHJ7YiT6qgZ+PFLIQ1NjGT8k4pqvm62rIk9vICK4OxFB3XF3u/bvfvWNJjRqddOQky1c+bU2WyzsOV7MVz9mU1JZj793NyqqG9AGejJrUl8Segfe1PE/+Oo4B07qGfRTQb39m7F4dGvf77vyPW09clWYEFa0+UA+ucXV3PuzGDzdXdBX1FFYWsO2wwVsPphPeFB3RsSFEBrgQYC3Oz7d3fhqZzZ7MouJj/bnF9P7U1xRx9d7cvlyRzYAqRP7XLdU4OJcy5UT7tdyvdKxFY1azW0JWkb2D2XXsSJ2Hyti6i09mDAsolWT+1d6YHJfjmeXk366lJhwn3aXinAO8n9RiCuUVtbx5Y5zDI4JZNrIHs3OTGrqjew/eXEBw3U7s5s9T6X66RLe0T1Rq1X4enWjX5Qf54urMaGid6ht16qzJxeNmnGDwxk3OLxdx/HxdOPB2/vxwVfHZRisE5FiEeIyiqLw8aYsVKiYMyW2xXBXd3dXfjYkgp8NiaCuwUR5dQMVVfWUVzcQFeJ11bONHqHeTjvU4QxuiQ9BrVYRa+NlXIT9SLEIcZl9J/QcO1fOA5P6Euh7/WVIPLq5ENHNhYig7nZK1zmpVCpGxLVcIl90XHLPeyF+UlNv5F+bT9FL682k4ZGOjiNEhyXFIsRPvt13nupaIw9NjbP7oo1CdCZSLEIAhjojmw/kMzwu5JqffhdCtI4UixDApv151DeamXFbT0dHEaLDk2IRXV5NvZEtB/NIjA0mMrjzXBIshKNIsYgupa7BRLauqtlj3+3Po67BzIzbejkolRCdi1xuLLoMi6LwzpqjnMitYECvAFIn9MHfpxvfHchjeL9gIq+ycKIQ4uZJsYguY+OeXE7kVjB6QCgZZ8tYsmIfkcFe1DWYmS5zK0JYjRSL6BLO5F/gy+3Z3BIfwmPJ/ampN5G2K4ctB/NJjA2WK8GEsCIpFtHp1dQb+eCrYwT4dOPnSXGoVCq8PFyZNakvd4yOxt1V4+iIQnQqMnkvOjVFUVj59UkqDY38MmVgi7sT+ni64SbFIoRVSbGITm3/ST0HT5Uwc1zvq97ISghhfVIsotOqazDxry2niQ71btVdDYUQ1iHFIjqtdTuzqTI0Miepn6z9JYQdSbGITilPb2DzgXzGDQknJtzX0XGE6FKkWESnY1EU/m9TFp7uLtwzPsbRcYTocqRYRKez62gRZ/IvcN/PYvDycHV0HCG6HCkW0akoikLa7hx6aX24bZDW0XGE6JKkWBzEaLJgNJkdHaPTyS2uRl9Rx/gh4ahVMmEvhCNIsdxAbb2RrPMVVj/uX9ce4w+rDmFRFKsfuyvbm1mMRq1ieGywo6MI0WVJsdxA+ulSlv8znfKqeqsds7yqniNnSskpquZQVkmL7blF1Xzxw1nMFovVXrMrsCgK+07oSegdSHd3mVuBFBsNAAAW50lEQVQRwlGkWG7g0uKEmTnWO2vZfbwIBQjw6cbandlYLP85a2kwmvnr2mNs2J3Lpv15VnvNruBM/gUqqhu4pX+Io6MI0aVJsdxARHB3vD1dOZFbbpXjKYrCzqNF9Iv05f4JfSgsrWHfyeKm7V/tzEZfWUePEC/W7simuLzWKq/bFew9UYybi5ohfYIcHUWILk2K5QbUKhXx0f5k5lagWGE+5FxhFcXltdyWoCUxLoSI4O6s25mD2WIht6iab/flMXaQlqfvG4yLRs3KjSdlHqYVzBYLB07qGdI3CHc3WbRbCEeSYmmF+Gh/Lhga0ZW1/+zhx6M63FzVJMaFoFapuGtML4rLa9l1tIgVG0/g5enK/RP74O/djdSJfcjKq2T74UIrvIvO7URuBdW1Rm6JD3V0FCG6PCmWVojvGQBc/OHVHkaTmb0n9AzvF4xHt4u/VQ/rF0yPUC8+/jaL88UG5tzer2nieewgLXE9/Fi97YxVLx7ojPZmFuPRzYWE3oGOjiJElyfF0gohfh4E+bqTmdO+eZb006XUNZi4LeE/H9xTqVTcNaY3ZovC0L5BzS6TValUPDwtDrNZ4eWPD7B2xzkqqhvalaEzMposHDpVwrB+Qbi6yLe0EI4mg9GtFB/tz8GsEiwWpc0r5f54tIgAn27ERfs3e3xwn0CemplAbA8/VFd8qC/E35MFqUNI253D+h9zSNuVy7B+QTw0LU4uqeXixRAbdudQ12BmpAyDCeEUpFhaKb6nPzsydOQWV9NLe/M3jKqobuBYdhl3jo5u8YlwlUrF0H7X/kBfvyg/FkQNQV9Zxw/pBXyz7zwh/p7c+7PrL7BoMlvI0xvoGebdorA6A0OdkY82nODwmVJGxIXQ/6chSyGEY9lt3CA7O5vU1FSSkpJITU0lJyenxT47d+5k5syZDBw4kOXLlzfb9sILL5CSktL0X1xcHFu2bLFTeoiPvvhDq63DYftPFKMocOvAtq9fFeLnwX0T+jAiLoSth/KpqTdec9+GRjN/+TyDl/9xgFXfnWr2WZnOIFtXxbIV+zl6rozZk/vyy5QBcs8VIZyE3YplyZIlzJ49m2+//ZbZs2ezePHiFvtERUXxyiuv8Oijj7bY9vrrr7Nu3TrWrVvH8uXL8fX1ZezYsfaIDoBvdzcigru3eQL/QFYJPUK8CAvwbHeWO0f3pL7RzJaD+VfdXltv5M3PDpOZU86QPkF8f6iAv649RqOxc6xN9sOhfP6w6iAAi+YMZ3JiVKc8IxOio7JLsZSVlZGZmUlycjIAycnJZGZmUl7e/Lf/6Oho+vfvj4vL9UfoPv/8c6ZPn46bm5vNMl9NfLQ/p/Mv3PTikeVV9ZwpuMDwOOt8IjwqxIshfYL4bn8e9Y2mZtuqahp5/Z/pZBdW8UTKQObfO4hZk/py6FQJb/778HXPcpydoiis35XDG58cpHe4L0v+a4Tcx14IJ2SXYtHpdISGhqLRaADQaDSEhISg0+lu+liNjY2sX7+ee+65x9oxb6h/dABGk4UzBVVX3Z51voJdx1q+p4OnLq4HNsJKxQJw563R1NSb2Jb+n8+4FJbW8IdPDlFUXsv8eweR+NPrTRkRxeMpA8jWVfHel8eslqG9FEXhgqGhVWdSJrOFFRtP8uX2c/xseCTPpg6Re60I4aQ63OT95s2bCQ8PJz4+/qafGxjo1a7Xvs3bnXe+PMrRnApuGxaF5qcxfUVRWPP9Gf6x4TgWBQbFhtLrstvhHjlbRk+tDwmx1rtqKTjYm8F9c/nuQB6pSXHsyyzirX+n083VhZd/eSv9ezX/PMedwd40WuCj9ce50GCmT6Rfs2M5wr++Pck/N2UB4OaixsvTjRB/D3qE+dAjzJsQfw9ydNVk5ZZz6vzFD0A+MCWWB6bEdsihL0d9ndurI+aWzI5ll2LRarUUFxdjNpvRaDSYzWb0ej1a7c1PZH/xxRdtPlspKzO0exJ7eL9gvtmdw9EzJcwc25v+PQNY+c1J9mYWM7xfMJm55axcf5wnZyYAF68GO5FdTsrYXpSUVLfrta80JTGKP/0rnd++vYMzBReIifDhV3cl4O/ldtXXGhYTyCduGlZ/l8Vjyf2Bi9/MJSXV7MzQsfVQPs/NGoqnu+2/LWrrjXz5wxlio/wY2DuAmnoThloj+so6dmUUsmnvxSE7FRAe3J2hfYMY2jeYwX2CUKlUVv9a2tqlr3NH0xFzS2brUatVbfqF3C7FEhgYSHx8PGlpaaSkpJCWlkZ8fDwBATd3eWhRUREHDx7kzTfftFHSG3s8ZQDDY4P5ckc2b685ikc3DfUNZn5+RzzjE8L46scc1u3MJreomugwbw6dKkEBEmOtv+JuXA8/YiJ8OFNwgUnDIkmd1AcXzbVHNz3dXRiToGVbegH3/SwGX69uwMV5mX9tOUVdg5mNe3Ptcp/4LQfzqWswM2tSX6LDmv+mpigKVbVGyi7Uow30bFqlQAjRMdjtqrClS5eyatUqkpKSWLVqFcuWLQNg3rx5HD16FIADBw4wbtw4VqxYwaeffsq4cePYsWNH0zG+/PJLJkyYgJ+f31Vfwx7UKhW3xIfyymO38PC0OCKCvXj6vkHcN6kfKpWK2xOj8Ozmwtod5wDYf1JPRFB3woO6Wz2LSqXiiZSBPP/AUB6c0u+6pXLJ5OGRWCwK36cXND22ZvtZGo0W4nr4sWl/ns2Xj6lvNPHdgXwGxQS2KBW4+L58u7vRO9xHSkWIDshu/2pjYmJYvXp1i8c//PDDpj8nJiayffv2ax7jiSeesEm2ttCo1YwbHM64weHNHvd0dyFpZA++3H6O9NMlnM6rZPptPW2WI8DHnQAf91bvHxrgyaCYQLalF3Dn6GjO5FWy44iOKbdEMWlYJC9+uIcvd5zj0Tv72yzzD4cLMdQZSb61p81eQwjhOLKwkg1MHh6Jl4crf1ufiYJ1rwazhttHRFFVa2RPZjF/W3sUb09Xpt/aiyA/DyYPj2LX0SLOF197vLfRaKbS0LY1y4wmM9/sPU9cDz/6RPje+AlCiA5HisUGPLq5MG1kDxoazWgDPW0yDNYe8dH+RAR351+bT3Mip5x7xsc0TdjfeWs0nu4urN52tsXzFEXhYJaeRX/bw4J3fmTx3/exZvs5snVV17xXjaHOSE5RVdNnf3Zm6LhQ08h0OVsRotOSAWwbmTgskh8OFzJucLjTXRp7aS5o5caT9Iny47ZB/7k6r7u7K9Nv7cmnW8/w3f48+kT6EuDjToPRzD+/O0XG2TKiQryYMDSCY9nlbNidQ9quHEYPCOXRO/s3W1aluKKWP/zfQapqjahVKrSBnlyoaSQm3KfFQpxCiM5DisVGurlp+MPjo5yuVC4Z1T+U03mVpCbFtVgUc8KwSLZn6PjXltPNHu/mpmHWxD5MSoxEo1aTfGtPDHVGvt13ng27c3HRqHlo2sXjVRoaePPTw1gUeOSOePSVdZwvrsZktnDP+Bin/boIIdpPisWGnPmHp5urhkeT+1/1+nlXFzWLH0qkqLyWsqp6yqsaqK03cluCtsWFAl4erk1FkbYrB1cXNXeP681///sw1bVGnn9gqCy7IkQXI8UirsrNVUOPUG96hLbu08B3j+2F0WTm2315HMgqoabOyG/uHyylIkQXJMUirEKlUnH/hD6YTApb0/N5fMYABsj9UYTokqRYhNWoVCoenNKPu8b1krtbCtGFyeXGwuqkVITo2qRYhBBCWJUUixBCCKuSYhFCCGFVUixCCCGsSopFCCGEVUmxCCGEsKou9TmWyxdI7IjHt5WOmFsy209HzC2ZraOtmVTKtdY7F0IIIdpAhsKEEEJYlRSLEEIIq5JiEUIIYVVSLEIIIaxKikUIIYRVSbEIIYSwKik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+ "text/plain": [
+ "<Figure size 432x288 with 1 Axes>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "learn.recorder.plot()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 28,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ " <div>\n",
+ " <style>\n",
+ " /* Turns off some styling */\n",
+ " progress {\n",
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+ " border: none;\n",
+ " /* Needs to be in here for Safari polyfill so background images work as expected. */\n",
+ " background-size: auto;\n",
+ " }\n",
+ " .progress-bar-interrupted, .progress-bar-interrupted::-webkit-progress-bar {\n",
+ " background: #F44336;\n",
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+ " </style>\n",
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+ " 0.00% [0/1 00:00<00:00]\n",
+ " </div>\n",
+ " \n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: left;\">\n",
+ " <th>epoch</th>\n",
+ " <th>train_loss</th>\n",
+ " <th>valid_loss</th>\n",
+ " <th>time</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " </tbody>\n",
+ "</table><p>\n",
+ "\n",
+ " <div>\n",
+ " <style>\n",
+ " /* Turns off some styling */\n",
+ " progress {\n",
+ " /* gets rid of default border in Firefox and Opera. */\n",
+ " border: none;\n",
+ " /* Needs to be in here for Safari polyfill so background images work as expected. */\n",
+ " background-size: auto;\n",
+ " }\n",
+ " .progress-bar-interrupted, .progress-bar-interrupted::-webkit-progress-bar {\n",
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+ " }\n",
+ " </style>\n",
+ " <progress value='0' class='progress-bar-interrupted' max='154', style='width:300px; height:20px; vertical-align: middle;'></progress>\n",
+ " Interrupted\n",
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+ " "
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "ename": "IndexError",
+ "evalue": "Traceback (most recent call last):\n File \"/home/serge/anaconda3/envs/bio-2/lib/python3.6/site-packages/torch/utils/data/_utils/worker.py\", line 99, in _worker_loop\n samples = collate_fn([dataset[i] for i in batch_indices])\n File \"/home/serge/anaconda3/envs/bio-2/lib/python3.6/site-packages/torch/utils/data/_utils/worker.py\", line 99, in <listcomp>\n samples = collate_fn([dataset[i] for i in batch_indices])\n File \"/home/serge/anaconda3/envs/bio-2/lib/python3.6/site-packages/fastai/data_block.py\", line 636, in __getitem__\n if self.item is None: x,y = self.x[idxs],self.y[idxs]\n File \"/home/serge/anaconda3/envs/bio-2/lib/python3.6/site-packages/fastai/data_block.py\", line 109, in __getitem__\n if isinstance(idxs, Integral): return self.get(idxs)\n File \"/home/serge/anaconda3/envs/bio-2/lib/python3.6/site-packages/fastai/data_block.py\", line 410, in get\n o = self.items[i]\nIndexError: index 17 is out of bounds for axis 0 with size 17\n",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mIndexError\u001b[0m Traceback (most recent call last)",
+ "\u001b[0;32m<ipython-input-28-8587f3539821>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mlearn\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+ "\u001b[0;32m~/anaconda3/envs/bio-2/lib/python3.6/site-packages/fastai/basic_train.py\u001b[0m in \u001b[0;36mfit\u001b[0;34m(self, epochs, lr, wd, callbacks)\u001b[0m\n\u001b[1;32m 197\u001b[0m \u001b[0mcallbacks\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mcb\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mcb\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcallback_fns\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mlistify\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdefaults\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mextra_callback_fns\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mlistify\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mcallbacks\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 198\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mdefaults\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mextra_callbacks\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mcallbacks\u001b[0m \u001b[0;34m+=\u001b[0m \u001b[0mdefaults\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mextra_callbacks\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 199\u001b[0;31m \u001b[0mfit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mepochs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmetrics\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmetrics\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcallbacks\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcallbacks\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0mcallbacks\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 200\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 201\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mcreate_opt\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlr\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0mFloats\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mwd\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0mFloats\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m0.\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m->\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m~/anaconda3/envs/bio-2/lib/python3.6/site-packages/fastai/basic_train.py\u001b[0m in \u001b[0;36mfit\u001b[0;34m(epochs, learn, callbacks, metrics)\u001b[0m\n\u001b[1;32m 104\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mcb_handler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mskip_validate\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mlearn\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mempty_val\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 105\u001b[0m val_loss = validate(learn.model, learn.data.valid_dl, loss_func=learn.loss_func,\n\u001b[0;32m--> 106\u001b[0;31m cb_handler=cb_handler, pbar=pbar)\n\u001b[0m\u001b[1;32m 107\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mval_loss\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 108\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mcb_handler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mon_epoch_end\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mval_loss\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;32mbreak\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m~/anaconda3/envs/bio-2/lib/python3.6/site-packages/fastai/basic_train.py\u001b[0m in \u001b[0;36mvalidate\u001b[0;34m(model, dl, loss_func, cb_handler, pbar, average, n_batch)\u001b[0m\n\u001b[1;32m 55\u001b[0m \u001b[0mval_losses\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mnums\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\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 56\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mcb_handler\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mcb_handler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mset_dl\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdl\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 57\u001b[0;31m \u001b[0;32mfor\u001b[0m \u001b[0mxb\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0myb\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mprogress_bar\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mparent\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mpbar\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mleave\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mpbar\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m)\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[0m\u001b[1;32m 58\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mcb_handler\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mxb\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0myb\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcb_handler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mon_batch_begin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mxb\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0myb\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtrain\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 59\u001b[0m \u001b[0mval_loss\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mloss_batch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmodel\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mxb\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0myb\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mloss_func\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcb_handler\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mcb_handler\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m~/anaconda3/envs/bio-2/lib/python3.6/site-packages/fastprogress/fastprogress.py\u001b[0m in \u001b[0;36m__iter__\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 70\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupdate\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[1;32m 71\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 72\u001b[0;31m \u001b[0;32mfor\u001b[0m \u001b[0mi\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mo\u001b[0m \u001b[0;32min\u001b[0m \u001b[0menumerate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_gen\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[0m\u001b[1;32m 73\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mi\u001b[0m \u001b[0;34m>=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtotal\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;32mbreak\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 74\u001b[0m \u001b[0;32myield\u001b[0m \u001b[0mo\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m~/anaconda3/envs/bio-2/lib/python3.6/site-packages/fastai/basic_data.py\u001b[0m in \u001b[0;36m__iter__\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 73\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m__iter__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\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 74\u001b[0m \u001b[0;34m\"Process and returns items from `DataLoader`.\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 75\u001b[0;31m \u001b[0;32mfor\u001b[0m \u001b[0mb\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdl\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;32myield\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mproc_batch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mb\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 76\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 77\u001b[0m \u001b[0;34m@\u001b[0m\u001b[0mclassmethod\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m~/anaconda3/envs/bio-2/lib/python3.6/site-packages/torch/utils/data/dataloader.py\u001b[0m in \u001b[0;36m__next__\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 566\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrcvd_idx\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreorder_dict\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 567\u001b[0m \u001b[0mbatch\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreorder_dict\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpop\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrcvd_idx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 568\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_process_next_batch\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbatch\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 569\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 570\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbatches_outstanding\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~/anaconda3/envs/bio-2/lib/python3.6/site-packages/torch/utils/data/dataloader.py\u001b[0m in \u001b[0;36m_process_next_batch\u001b[0;34m(self, batch)\u001b[0m\n\u001b[1;32m 606\u001b[0m \u001b[0;32mraise\u001b[0m \u001b[0mException\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"KeyError:\"\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mbatch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexc_msg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 607\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 608\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mbatch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexc_type\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbatch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexc_msg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 609\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mbatch\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 610\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;31mIndexError\u001b[0m: Traceback (most recent call last):\n File \"/home/serge/anaconda3/envs/bio-2/lib/python3.6/site-packages/torch/utils/data/_utils/worker.py\", line 99, in _worker_loop\n samples = collate_fn([dataset[i] for i in batch_indices])\n File \"/home/serge/anaconda3/envs/bio-2/lib/python3.6/site-packages/torch/utils/data/_utils/worker.py\", line 99, in <listcomp>\n samples = collate_fn([dataset[i] for i in batch_indices])\n File \"/home/serge/anaconda3/envs/bio-2/lib/python3.6/site-packages/fastai/data_block.py\", line 636, in __getitem__\n if self.item is None: x,y = self.x[idxs],self.y[idxs]\n File \"/home/serge/anaconda3/envs/bio-2/lib/python3.6/site-packages/fastai/data_block.py\", line 109, in __getitem__\n if isinstance(idxs, Integral): return self.get(idxs)\n File \"/home/serge/anaconda3/envs/bio-2/lib/python3.6/site-packages/fastai/data_block.py\", line 410, in get\n o = self.items[i]\nIndexError: index 17 is out of bounds for axis 0 with size 17\n"
+ ]
+ }
+ ],
+ "source": [
+ "learn.fit(1)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "> \u001b[0;32m/home/serge/anaconda3/envs/bio-2/lib/python3.6/site-packages/torch/utils/data/dataloader.py\u001b[0m(608)\u001b[0;36m_process_next_batch\u001b[0;34m()\u001b[0m\n",
+ "\u001b[0;32m 606 \u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mException\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"KeyError:\"\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mbatch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexc_msg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0m\u001b[0;32m 607 \u001b[0;31m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0m\u001b[0;32m--> 608 \u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mbatch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexc_type\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbatch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexc_msg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0m\u001b[0;32m 609 \u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mbatch\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0m\u001b[0;32m 610 \u001b[0;31m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0m\n",
+ "ipdb> batch\n",
+ "<torch.utils.data._utils.ExceptionWrapper object at 0x7ff4d40b8b38>\n"
+ ]
+ }
+ ],
+ "source": [
+ "%debug"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 62,
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: left;\">\n",
+ " <th>epoch</th>\n",
+ " <th>train_loss</th>\n",
+ " <th>valid_loss</th>\n",
+ " <th>accuracy</th>\n",
+ " <th>time</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <td>0</td>\n",
+ " <td>1.999583</td>\n",
+ " <td>2.891428</td>\n",
+ " <td>0.076797</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>1</td>\n",
+ " <td>1.996683</td>\n",
+ " <td>2.909333</td>\n",
+ " <td>0.076797</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>2</td>\n",
+ " <td>1.993628</td>\n",
+ " <td>2.928375</td>\n",
+ " <td>0.071895</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>3</td>\n",
+ " <td>1.988448</td>\n",
+ " <td>2.976008</td>\n",
+ " <td>0.096405</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>4</td>\n",
+ " <td>1.975731</td>\n",
+ " <td>2.991736</td>\n",
+ " <td>0.078431</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>5</td>\n",
+ " <td>1.962745</td>\n",
+ " <td>3.063164</td>\n",
+ " <td>0.099673</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>6</td>\n",
+ " <td>1.937906</td>\n",
+ " <td>3.158804</td>\n",
+ " <td>0.102941</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>7</td>\n",
+ " <td>1.915476</td>\n",
+ " <td>3.222555</td>\n",
+ " <td>0.120915</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>8</td>\n",
+ " <td>1.889667</td>\n",
+ " <td>3.251005</td>\n",
+ " <td>0.101307</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>9</td>\n",
+ " <td>1.861332</td>\n",
+ " <td>3.390323</td>\n",
+ " <td>0.106209</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>10</td>\n",
+ " <td>1.833662</td>\n",
+ " <td>3.394011</td>\n",
+ " <td>0.081699</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>11</td>\n",
+ " <td>1.812667</td>\n",
+ " <td>3.366220</td>\n",
+ " <td>0.104575</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>12</td>\n",
+ " <td>1.785382</td>\n",
+ " <td>3.465658</td>\n",
+ " <td>0.088235</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>13</td>\n",
+ " <td>1.761000</td>\n",
+ " <td>3.564012</td>\n",
+ " <td>0.089869</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>14</td>\n",
+ " <td>1.740894</td>\n",
+ " <td>3.674994</td>\n",
+ " <td>0.104575</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>15</td>\n",
+ " <td>1.721406</td>\n",
+ " <td>3.705786</td>\n",
+ " <td>0.068627</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>16</td>\n",
+ " <td>1.700805</td>\n",
+ " <td>3.702142</td>\n",
+ " <td>0.066993</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>17</td>\n",
+ " <td>1.684734</td>\n",
+ " <td>3.788021</td>\n",
+ " <td>0.066993</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>18</td>\n",
+ " <td>1.674555</td>\n",
+ " <td>3.792717</td>\n",
+ " <td>0.070261</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>19</td>\n",
+ " <td>1.664761</td>\n",
+ " <td>3.812120</td>\n",
+ " <td>0.083333</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>20</td>\n",
+ " <td>1.652747</td>\n",
+ " <td>3.813709</td>\n",
+ " <td>0.070261</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>21</td>\n",
+ " <td>1.646771</td>\n",
+ " <td>3.840080</td>\n",
+ " <td>0.063725</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>22</td>\n",
+ " <td>1.643901</td>\n",
+ " <td>3.840845</td>\n",
+ " <td>0.066993</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>23</td>\n",
+ " <td>1.641238</td>\n",
+ " <td>3.841465</td>\n",
+ " <td>0.066993</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>24</td>\n",
+ " <td>1.643271</td>\n",
+ " <td>3.844751</td>\n",
+ " <td>0.065359</td>\n",
+ " <td>00:00</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "learn.fit_one_cycle(25)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "CPU times: user 42min 11s, sys: 8min 41s, total: 50min 52s\n",
+ "Wall time: 1h 25min 43s\n"
+ ]
+ }
+ ],
+ "source": [
+ "processors = [\n",
+ " sequence.GSFileProcessor(),\n",
+ " sequence.GSTokenizeProcessor(tokenizer=sequence.GSTokenizer(ngram=8, skip=0, n_cpus=4)),\n",
+ " sequence.Dna2VecProcessor()]\n",
+ "%time for p in processors: p.process(data)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "1686"
+ ]
+ },
+ "execution_count": 10,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "len(data.items)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Genome vectors"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
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+ " array([-10894.013 , 139155.39 , -7461.7837, -48455.723 , ..., -18387.576 , -48287.562 , -53913.57 , -17648.615 ],\n",
+ " dtype=float32),\n",
+ " array([ -821.4669, 151978.92 , -3094.6824, -48929.207 , ..., -6454.1875, -47306.59 , -58581.387 , -23744.344 ],\n",
+ " dtype=float32),\n",
+ " array([-10386.709, 145556.66 , -8388.681, -51004.363, ..., -19887.713, -50264.78 , -55312.555, -18267.414],\n",
+ " dtype=float32),\n",
+ " array([-10954.063, 144915.73 , -8300.826, -50466.55 , ..., -18784.277, -49640.176, -55164.33 , -18075.064],\n",
+ " dtype=float32),\n",
+ " array([-10476.142, 138501.66 , -7601.43 , -48551.77 , ..., -18133.258, -47410.016, -53265.05 , -17589.61 ],\n",
+ " dtype=float32),\n",
+ " array([ -2129.5483, 144000.16 , -3646.6157, -47242.992 , ..., -10461.203 , -47674.57 , -56220.39 , -19774.756 ],\n",
+ " dtype=float32),\n",
+ " array([ -1789.322 , 145023. , -3882.7065, -47203.53 , ..., -10953.228 , -47194.184 , -57300.18 , -18991.203 ],\n",
+ " dtype=float32),\n",
+ " array([ -9015.164, 132998.44 , -7283.794, -46476.316, ..., -17287.709, -45436.227, -50719.8 , -17184.012],\n",
+ " dtype=float32),\n",
+ " array([ -6949.803, 107936.19 , 3876.474, -30740.477, ..., -25815.416, -42259.34 , -34216.33 , -14356.996],\n",
+ " dtype=float32),\n",
+ " array([ -2805.2156, 150145.42 , -4451.0806, -49853.88 , ..., -11119.602 , -49216.28 , -58772.645 , -19955.117 ],\n",
+ " dtype=float32),\n",
+ " array([-11356.179, 143684.17 , -7926.552, -50246.203, ..., -18394.355, -48898.344, -54961.938, -18206.752],\n",
+ " dtype=float32),\n",
+ " array([-10341.07 , 140623.98 , -7953.529, -48878.266, ..., -18675.309, -47791.426, -53565.125, -17611.18 ],\n",
+ " dtype=float32),\n",
+ " ...]"
+ ]
+ },
+ "execution_count": 11,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "data.items"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def log_scale(X):\n",
+ " x=np.asarray(X);e=1e-6\n",
+ " return np.log10(x+np.abs(x.min())+e) \n",
+ "\n",
+ "\n",
+ "x=np.asarray(data.items)\n",
+ "bad_fastas = np.where(np.mean(x,axis=1) == 0.)[0]\n",
+ "X = np.delete(x, bad_fastas,0)\n",
+ "labelList=[\" \".join(i.split()[1:3]) for i in data.descriptions]\n",
+ "labelList=np.delete(np.asarray(labelList), bad_fastas)\n",
+ "vocab=list(np.unique(labelList))\n",
+ "y=[vocab.index(x) for x in labelList]"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Correlation Distance in log-scaled space"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### tSNE"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 18,
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "CPU times: user 31.1 s, sys: 313 ms, total: 31.4 s\n",
+ "Wall time: 30.9 s\n"
+ ]
+ }
+ ],
+ "source": [
+ "tsne = manifold.TSNE(n_components=3, init='pca', perplexity=10, metric=\"correlation\",random_state=0)\n",
+ "%time X3 = tsne.fit_transform(log_scale(X))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 19,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "genus = [i.split()[0] for i in labelList]\n",
+ "genus_vocab=list(np.unique(genus))\n",
+ "y=[genus_vocab.index(x) for x in genus]\n",
+ "genus_vocab\n",
+ "\n",
+ "X3_df = pd.DataFrame(data=X3, columns=[\"pc1\",'pc2','pc3'], index=labelList)\n",
+ "\n",
+ "X3_df[\"genus\"]=genus\n",
+ "X3_df[\"y\"]=y\n",
+ "\n",
+ "genus_df=X3_df.groupby(\"genus\").agg({\"pc1\": list, \"pc2\":list,\"pc3\":list,\"y\":np.mean})"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Correlation Distance visualisation"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 20,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/home/serge/anaconda3/envs/bio/lib/python3.6/site-packages/IPython/core/display.py:689: UserWarning:\n",
+ "\n",
+ "Consider using IPython.display.IFrame instead\n",
+ "\n"
+ ]
+ },
+ {
+ "data": {
+ "text/html": [
+ "<iframe id=\"igraph\" scrolling=\"no\" style=\"border:none;\" seamless=\"seamless\" src=\"https://plot.ly/~sergeman/12.embed\" height=\"1000px\" width=\"1000px\"></iframe>"
+ ],
+ "text/plain": [
+ "<plotly.tools.PlotlyDisplay object>"
+ ]
+ },
+ "execution_count": 20,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "data=[]\n",
+ "for g in genus_df.index:\n",
+ " trace = go.Scatter3d(\n",
+ " name = str(g),\n",
+ " x=genus_df.loc[g,\"pc1\"],\n",
+ " y=genus_df.loc[g,\"pc2\"],\n",
+ " z=genus_df.loc[g,\"pc3\"],\n",
+ " mode='markers',\n",
+ " marker=dict(\n",
+ " size=8,\n",
+ " color=genus_df.loc[g,\"y\"], # set color to an array/list of desired values\n",
+ " colorscale='Jet', # choose a colorscale\n",
+ " opacity=0.5)\n",
+ " )\n",
+ "\n",
+ " data.append(trace)\n",
+ " \n",
+ "\n",
+ "layout = go.Layout(\n",
+ " width=1000,\n",
+ " height=1000,\n",
+ " margin=dict(\n",
+ " l=0,\n",
+ " r=0,\n",
+ " b=0,\n",
+ " t=0\n",
+ " )\n",
+ ")\n",
+ "fig = go.Figure(data=data, layout=layout)\n",
+ "py.iplot(fig, filename='correlation distance ncbi-genomes-2019-04-07 Escherichia,Klebsiella,Bacillus')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Eucleadian Distance in log-scaled space"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### tSNE"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 21,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "CPU times: user 25.8 s, sys: 334 ms, total: 26.1 s\n",
+ "Wall time: 25.5 s\n"
+ ]
+ }
+ ],
+ "source": [
+ "tsne = manifold.TSNE(n_components=3, init='pca', perplexity=30,random_state=0)\n",
+ "%time X3 = tsne.fit_transform(log_scale(X))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 22,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "genus = [i.split()[0] for i in labelList]\n",
+ "genus_vocab=list(np.unique(genus))\n",
+ "y=[genus_vocab.index(x) for x in genus]\n",
+ "genus_vocab\n",
+ "\n",
+ "X3_df = pd.DataFrame(data=X3, columns=[\"pc1\",'pc2','pc3'], index=labelList)\n",
+ "\n",
+ "X3_df[\"genus\"]=genus\n",
+ "X3_df[\"y\"]=y\n",
+ "\n",
+ "genus_df=X3_df.groupby(\"genus\").agg({\"pc1\": list, \"pc2\":list,\"pc3\":list,\"y\":np.mean})"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Eucleadian Distance Visualisation"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 32,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/home/serge/anaconda3/envs/bio/lib/python3.6/site-packages/IPython/core/display.py:689: UserWarning:\n",
+ "\n",
+ "Consider using IPython.display.IFrame instead\n",
+ "\n"
+ ]
+ },
+ {
+ "data": {
+ "text/html": [
+ "<iframe id=\"igraph\" scrolling=\"no\" style=\"border:none;\" seamless=\"seamless\" src=\"https://plot.ly/~sergeman/14.embed\" height=\"1000px\" width=\"1000px\"></iframe>"
+ ],
+ "text/plain": [
+ "<plotly.tools.PlotlyDisplay object>"
+ ]
+ },
+ "execution_count": 32,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "data=[]\n",
+ "for g in genus_df.index:\n",
+ " trace = go.Scatter3d(\n",
+ " name = str(g),\n",
+ " x=genus_df.loc[g,\"pc1\"],\n",
+ " y=genus_df.loc[g,\"pc2\"],\n",
+ " z=genus_df.loc[g,\"pc3\"],\n",
+ " mode='markers',\n",
+ " marker=dict(\n",
+ " size=8,\n",
+ " color=genus_df.loc[g,\"y\"]+1, # set color to an array/list of desired values\n",
+ " colorscale='YlGnBu', # choose a colorscale\n",
+ " opacity=0.5)\n",
+ " )\n",
+ "\n",
+ " data.append(trace)\n",
+ " \n",
+ "\n",
+ "layout = go.Layout(\n",
+ " width=1000,\n",
+ " height=1000,\n",
+ " margin=dict(\n",
+ " l=0,\n",
+ " r=0,\n",
+ " b=0,\n",
+ " t=0\n",
+ " )\n",
+ ")\n",
+ "fig = go.Figure(data=data, layout=layout)\n",
+ "py.iplot(fig, filename='eucledian distance metric by genus Escherichia|Klebsiella|Bacillus')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Eucleadian Distance in unmodified space"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### tSNE"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 27,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "CPU times: user 41.5 s, sys: 313 ms, total: 41.8 s\n",
+ "Wall time: 41.2 s\n"
+ ]
+ }
+ ],
+ "source": [
+ "tsne = manifold.TSNE(n_components=3, init='pca', perplexity=30,random_state=0)\n",
+ "%time X3 = tsne.fit_transform(X)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 28,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "genus = [i.split()[0] for i in labelList]\n",
+ "genus_vocab=list(np.unique(genus))\n",
+ "y=[genus_vocab.index(x) for x in genus]\n",
+ "genus_vocab\n",
+ "\n",
+ "X3_df = pd.DataFrame(data=X3, columns=[\"pc1\",'pc2','pc3'], index=labelList)\n",
+ "\n",
+ "X3_df[\"genus\"]=genus\n",
+ "X3_df[\"y\"]=y\n",
+ "\n",
+ "genus_df=X3_df.groupby(\"genus\").agg({\"pc1\": list, \"pc2\":list,\"pc3\":list,\"y\":np.mean})"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Eucleadian Distance Visualisation"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 29,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/home/serge/anaconda3/envs/bio/lib/python3.6/site-packages/IPython/core/display.py:689: UserWarning:\n",
+ "\n",
+ "Consider using IPython.display.IFrame instead\n",
+ "\n"
+ ]
+ },
+ {
+ "data": {
+ "text/html": [
+ "<iframe id=\"igraph\" scrolling=\"no\" style=\"border:none;\" seamless=\"seamless\" src=\"https://plot.ly/~sergeman/16.embed\" height=\"1000px\" width=\"1000px\"></iframe>"
+ ],
+ "text/plain": [
+ "<plotly.tools.PlotlyDisplay object>"
+ ]
+ },
+ "execution_count": 29,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "data=[]\n",
+ "for g in genus_df.index:\n",
+ " trace = go.Scatter3d(\n",
+ " name = str(g),\n",
+ " x=genus_df.loc[g,\"pc1\"],\n",
+ " y=genus_df.loc[g,\"pc2\"],\n",
+ " z=genus_df.loc[g,\"pc3\"],\n",
+ " mode='markers',\n",
+ " marker=dict(\n",
+ " size=8,\n",
+ " color=genus_df.loc[g,\"y\"], # set color to an array/list of desired values\n",
+ " colorscale='Jet', # choose a colorscale\n",
+ " opacity=0.5)\n",
+ " )\n",
+ "\n",
+ " data.append(trace)\n",
+ " \n",
+ "\n",
+ "layout = go.Layout(\n",
+ " width=1000,\n",
+ " height=1000,\n",
+ " margin=dict(\n",
+ " l=0,\n",
+ " r=0,\n",
+ " b=0,\n",
+ " t=0\n",
+ " )\n",
+ ")\n",
+ "fig = go.Figure(data=data, layout=layout)\n",
+ "py.iplot(fig, filename='eucledian distance in native space Escherichia|Klebsiella|Bacillus')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Genome Inventory"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "all_fastas = sequence.Dna2VecList.from_folder(DB)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 28,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "{'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_003261035.1_ASM326103v1_genomic.fna',\n",
+ " 'description': 'NZ_CP030062.1 Mannheimia varigena strain Teagasc 1 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP030062.1',\n",
+ " 'name': 'NZ_CP030062.1'}"
+ ]
+ },
+ "execution_count": 28,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "next(iter(all_fastas))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 30,
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [],
+ "source": [
+ "a = [x for x in all_fastas if \"plasmid\" not in x['description'].split()] "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 31,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "[{'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_003261035.1_ASM326103v1_genomic.fna',\n",
+ " 'description': 'NZ_CP030062.1 Mannheimia varigena strain Teagasc 1 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP030062.1',\n",
+ " 'name': 'NZ_CP030062.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000750395.2_ASM75039v2_genomic.fna',\n",
+ " 'description': 'NZ_CP009085.2 Salmonella enterica subsp. enterica serovar Enteritidis strain OLF-SE3-98983-4, complete genome',\n",
+ " 'id': 'NZ_CP009085.2',\n",
+ " 'name': 'NZ_CP009085.2'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900205745.1_Lf_IMDO_130101_genomic.fna',\n",
+ " 'description': 'NZ_LT906621.1 Lactobacillus fermentum strain IMDO 130101 genome assembly, chromosome: I',\n",
+ " 'id': 'NZ_LT906621.1',\n",
+ " 'name': 'NZ_LT906621.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001854145.2_ASM185414v2_genomic.fna',\n",
+ " 'description': 'NZ_CP017188.2 Xanthomonas citri pv. glycines str. 8ra chromosome, complete genome',\n",
+ " 'id': 'NZ_CP017188.2',\n",
+ " 'name': 'NZ_CP017188.2'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_002240155.1_ASM224015v1_genomic.fna',\n",
+ " 'description': 'NZ_CP022223.1 Mycobacterium chimaera strain SJ42 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP022223.1',\n",
+ " 'name': 'NZ_CP022223.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000056065.1_ASM5606v1_genomic.fna',\n",
+ " 'description': 'NC_008054.1 Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 complete genome',\n",
+ " 'id': 'NC_008054.1',\n",
+ " 'name': 'NC_008054.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900324205.1_1_1439_genomic.fna',\n",
+ " 'description': 'NZ_LT992456.1 Staphylococcus aureus isolate 1_1439 genome assembly, chromosome: I',\n",
+ " 'id': 'NZ_LT992456.1',\n",
+ " 'name': 'NZ_LT992456.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900324205.1_1_1439_genomic.fna',\n",
+ " 'description': 'NZ_LT992457.1 Staphylococcus aureus isolate 1_1439 genome assembly, plasmid: II',\n",
+ " 'id': 'NZ_LT992457.1',\n",
+ " 'name': 'NZ_LT992457.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001618685.1_ASM161868v1_genomic.fna',\n",
+ " 'description': 'NZ_CP014342.1 Geobacillus subterraneus strain KCTC 3922, complete genome',\n",
+ " 'id': 'NZ_CP014342.1',\n",
+ " 'name': 'NZ_CP014342.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001307295.1_ASM130729v1_genomic.fna',\n",
+ " 'description': 'NZ_CP012700.1 Sphingopyxis macrogoltabida strain EY-1, complete genome',\n",
+ " 'id': 'NZ_CP012700.1',\n",
+ " 'name': 'NZ_CP012700.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000183115.1_ASM18311v1_genomic.fna',\n",
+ " 'description': 'NC_014733.1 Methylovorus sp. MP688, complete genome',\n",
+ " 'id': 'NC_014733.1',\n",
+ " 'name': 'NC_014733.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_002838225.1_ASM283822v1_genomic.fna',\n",
+ " 'description': 'NZ_CP021390.1 Bifidobacterium breve strain DRBB26 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP021390.1',\n",
+ " 'name': 'NZ_CP021390.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001611975.1_ASM161197v1_genomic.fna',\n",
+ " 'description': 'NZ_CP014525.1 Haematospirillum jordaniae strain H5569, complete genome',\n",
+ " 'id': 'NZ_CP014525.1',\n",
+ " 'name': 'NZ_CP014525.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_002024245.1_ASM202424v1_genomic.fna',\n",
+ " 'description': 'NZ_CP019970.1 Enterococcus faecium isolate 2014-VREF-114 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP019970.1',\n",
+ " 'name': 'NZ_CP019970.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000367205.1_ASM36720v1_genomic.fna',\n",
+ " 'description': 'NC_021064.1 Cutibacterium avidum 44067, complete genome',\n",
+ " 'id': 'NC_021064.1',\n",
+ " 'name': 'NC_021064.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_002753405.1_ASM275340v1_genomic.fna',\n",
+ " 'description': 'NZ_CP024549.1 Klebsiella pneumoniae strain INF163 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP024549.1',\n",
+ " 'name': 'NZ_CP024549.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000008225.1_ASM822v1_genomic.fna',\n",
+ " 'description': 'NC_007332.1 Mycoplasma hyopneumoniae 7448, complete genome',\n",
+ " 'id': 'NC_007332.1',\n",
+ " 'name': 'NC_007332.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001448785.2_ASM144878v2_genomic.fna',\n",
+ " 'description': 'NZ_CP030175.1 Salmonella enterica subsp. enterica serovar Milwaukee str. SA19950795 chromosome, complete genome',\n",
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+ " 'id': 'NZ_CP020853.1',\n",
+ " 'name': 'NZ_CP020853.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_003812085.1_ASM381208v1_genomic.fna',\n",
+ " 'description': 'NZ_CP033756.1 Klebsiella pneumoniae strain FDAARGOS_566 chromosome 1, complete sequence',\n",
+ " 'id': 'NZ_CP033756.1',\n",
+ " 'name': 'NZ_CP033756.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_003812085.1_ASM381208v1_genomic.fna',\n",
+ " 'description': 'NZ_CP033757.1 Klebsiella pneumoniae strain FDAARGOS_566 chromosome 2',\n",
+ " 'id': 'NZ_CP033757.1',\n",
+ " 'name': 'NZ_CP033757.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_003288135.1_ASM328813v1_genomic.fna',\n",
+ " 'description': 'NZ_CP023566.1 Lactobacillus murinus strain CR141 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP023566.1',\n",
+ " 'name': 'NZ_CP023566.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900236425.1_Bru_genome11_genomic.fna',\n",
+ " 'description': 'NZ_LT962922.1 Brucella melitensis isolate 1 genome assembly, chromosome: 1',\n",
+ " 'id': 'NZ_LT962922.1',\n",
+ " 'name': 'NZ_LT962922.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900236425.1_Bru_genome11_genomic.fna',\n",
+ " 'description': 'NZ_LT962923.1 Brucella melitensis isolate 1 genome assembly, chromosome: 2',\n",
+ " 'id': 'NZ_LT962923.1',\n",
+ " 'name': 'NZ_LT962923.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001307525.1_ASM130752v1_genomic.fna',\n",
+ " 'description': 'NZ_CP011400.1 Bordetella pertussis strain B3629, complete genome',\n",
+ " 'id': 'NZ_CP011400.1',\n",
+ " 'name': 'NZ_CP011400.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001908295.1_ASM190829v1_genomic.fna',\n",
+ " 'description': 'NZ_CP018677.1 Acinetobacter baumannii strain LAC4, complete genome',\n",
+ " 'id': 'NZ_CP018677.1',\n",
+ " 'name': 'NZ_CP018677.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000318785.1_ASM31878v1_genomic.fna',\n",
+ " 'description': 'NC_020940.1 Chlamydia trachomatis Ia/SotonIa3 complete genome',\n",
+ " 'id': 'NC_020940.1',\n",
+ " 'name': 'NC_020940.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000829055.1_ASM82905v1_genomic.fna',\n",
+ " 'description': 'NZ_AP012544.1 Lactobacillus casei subsp. casei ATCC 393 DNA, complete genome',\n",
+ " 'id': 'NZ_AP012544.1',\n",
+ " 'name': 'NZ_AP012544.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001984445.1_ASM198444v1_genomic.fna',\n",
+ " 'description': 'NZ_CP019457.1 Streptomyces lydicus strain GS93 isolate 23 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP019457.1',\n",
+ " 'name': 'NZ_CP019457.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_002155145.1_ASM215514v1_genomic.fna',\n",
+ " 'description': 'NZ_CP021323.1 Kushneria konosiri strain X49, complete genome',\n",
+ " 'id': 'NZ_CP021323.1',\n",
+ " 'name': 'NZ_CP021323.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000759555.1_ASM75955v1_genomic.fna',\n",
+ " 'description': 'NZ_CP009046.1 Staphylococcus epidermidis strain SEI, complete genome',\n",
+ " 'id': 'NZ_CP009046.1',\n",
+ " 'name': 'NZ_CP009046.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000759555.1_ASM75955v1_genomic.fna',\n",
+ " 'description': 'NZ_CP009047.1 Staphylococcus epidermidis strain SEI plasmid, complete sequence',\n",
+ " 'id': 'NZ_CP009047.1',\n",
+ " 'name': 'NZ_CP009047.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000770155.1_ASM77015v1_genomic.fna',\n",
+ " 'description': 'NZ_CP009756.1 Enterobacter cloacae strain GGT036, complete genome',\n",
+ " 'id': 'NZ_CP009756.1',\n",
+ " 'name': 'NZ_CP009756.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001263395.1_ASM126339v1_genomic.fna',\n",
+ " 'description': 'NZ_CP011786.1 Bifidobacterium actinocoloniiforme DSM 22766, complete genome',\n",
+ " 'id': 'NZ_CP011786.1',\n",
+ " 'name': 'NZ_CP011786.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001442475.1_ASM144247v1_genomic.fna',\n",
+ " 'description': 'NZ_CP013133.1 Rickettsia rhipicephali strain HJ#5, complete genome',\n",
+ " 'id': 'NZ_CP013133.1',\n",
+ " 'name': 'NZ_CP013133.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900635825.1_34347_F01_genomic.fna',\n",
+ " 'description': 'NZ_LR134176.1 Legionella pneumophila strain NCTC12179 genome assembly, chromosome: 1',\n",
+ " 'id': 'NZ_LR134176.1',\n",
+ " 'name': 'NZ_LR134176.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000008945.1_ASM894v1_genomic.fna',\n",
+ " 'description': 'NC_010816.1 Bifidobacterium longum DJO10A, complete genome',\n",
+ " 'id': 'NC_010816.1',\n",
+ " 'name': 'NC_010816.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900639595.1_E8377_hybrid_assembly_genomic.fna',\n",
+ " 'description': 'NZ_LR135401.1 Enterococcus faecium isolate E8377 genome assembly, chromosome: 1',\n",
+ " 'id': 'NZ_LR135401.1',\n",
+ " 'name': 'NZ_LR135401.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900639595.1_E8377_hybrid_assembly_genomic.fna',\n",
+ " 'description': 'NZ_LR135402.1 Enterococcus faecium isolate E8377 genome assembly, plasmid: 2',\n",
+ " 'id': 'NZ_LR135402.1',\n",
+ " 'name': 'NZ_LR135402.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900639595.1_E8377_hybrid_assembly_genomic.fna',\n",
+ " 'description': 'NZ_LR135403.1 Enterococcus faecium isolate E8377 genome assembly, plasmid: 3',\n",
+ " 'id': 'NZ_LR135403.1',\n",
+ " 'name': 'NZ_LR135403.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900639595.1_E8377_hybrid_assembly_genomic.fna',\n",
+ " 'description': 'NZ_LR135404.1 Enterococcus faecium isolate E8377 genome assembly, plasmid: 4',\n",
+ " 'id': 'NZ_LR135404.1',\n",
+ " 'name': 'NZ_LR135404.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900639595.1_E8377_hybrid_assembly_genomic.fna',\n",
+ " 'description': 'NZ_LR135405.1 Enterococcus faecium isolate E8377 genome assembly, plasmid: 5',\n",
+ " 'id': 'NZ_LR135405.1',\n",
+ " 'name': 'NZ_LR135405.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900639595.1_E8377_hybrid_assembly_genomic.fna',\n",
+ " 'description': 'NZ_LR135406.1 Enterococcus faecium isolate E8377 genome assembly, plasmid: 6',\n",
+ " 'id': 'NZ_LR135406.1',\n",
+ " 'name': 'NZ_LR135406.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900639595.1_E8377_hybrid_assembly_genomic.fna',\n",
+ " 'description': 'NZ_LR135407.1 Enterococcus faecium isolate E8377 genome assembly, plasmid: 7',\n",
+ " 'id': 'NZ_LR135407.1',\n",
+ " 'name': 'NZ_LR135407.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001558475.2_ASM155847v2_genomic.fna',\n",
+ " 'description': 'NZ_CP014042.2 Vibrio mimicus strain ATCC 33654 chromosome 1, complete sequence',\n",
+ " 'id': 'NZ_CP014042.2',\n",
+ " 'name': 'NZ_CP014042.2'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001558475.2_ASM155847v2_genomic.fna',\n",
+ " 'description': 'NZ_CP014043.2 Vibrio mimicus strain ATCC 33654 chromosome 2, complete sequence',\n",
+ " 'id': 'NZ_CP014043.2',\n",
+ " 'name': 'NZ_CP014043.2'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001766335.1_ASM176633v1_genomic.fna',\n",
+ " 'description': 'NZ_CP016873.1 Legionella pneumophila subsp. pneumophila strain FFI105 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP016873.1',\n",
+ " 'name': 'NZ_CP016873.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_002844165.1_ASM284416v1_genomic.fna',\n",
+ " 'description': 'NZ_CP022407.1 Escherichia coli O121:H19 strain 16-9255 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP022407.1',\n",
+ " 'name': 'NZ_CP022407.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_002356015.1_ASM235601v1_genomic.fna',\n",
+ " 'description': 'NZ_AP017901.1 Mycobacterium tuberculosis DNA, complete genome, strain: NCGM946K2',\n",
+ " 'id': 'NZ_AP017901.1',\n",
+ " 'name': 'NZ_AP017901.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001021915.1_ASM102191v1_genomic.fna',\n",
+ " 'description': 'NZ_CP007810.1 Xanthomonas oryzae pv. oryzicola strain YM15, complete genome',\n",
+ " 'id': 'NZ_CP007810.1',\n",
+ " 'name': 'NZ_CP007810.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900475165.1_42731_D01_genomic.fna',\n",
+ " 'description': 'NZ_LS483356.1 Streptococcus pyogenes strain NCTC8230 genome assembly, chromosome: 1',\n",
+ " 'id': 'NZ_LS483356.1',\n",
+ " 'name': 'NZ_LS483356.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_003265245.1_ASM326524v1_genomic.fna',\n",
+ " 'description': 'NZ_CP022672.1 Shigella sonnei strain 866 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP022672.1',\n",
+ " 'name': 'NZ_CP022672.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001900335.1_ASM190033v1_genomic.fna',\n",
+ " 'description': 'NZ_CP010132.1 Escherichia coli strain C10, complete genome',\n",
+ " 'id': 'NZ_CP010132.1',\n",
+ " 'name': 'NZ_CP010132.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001618825.1_ASM161882v1_genomic.fna',\n",
+ " 'description': 'NZ_CP015062.1 Mesorhizobium ciceri strain CC1192 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP015062.1',\n",
+ " 'name': 'NZ_CP015062.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001548435.1_ASM154843v1_genomic.fna',\n",
+ " 'description': 'NZ_AP017308.1 Leptolyngbya sp. NIES-3755 DNA, complete genome',\n",
+ " 'id': 'NZ_AP017308.1',\n",
+ " 'name': 'NZ_AP017308.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_003111765.1_ASM311176v1_genomic.fna',\n",
+ " 'description': 'NZ_CP027862.1 Actinomyces sp. Z16 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP027862.1',\n",
+ " 'name': 'NZ_CP027862.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_002865505.1_ASM286550v1_genomic.fna',\n",
+ " 'description': 'NZ_CP025542.1 Pseudomonas fluorescens strain 2P24 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP025542.1',\n",
+ " 'name': 'NZ_CP025542.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000968195.1_ASM96819v1_genomic.fna',\n",
+ " 'description': 'NZ_FO704550.1 Xenorhabdus doucetiae str. FRM16 chromosome, complete genome',\n",
+ " 'id': 'NZ_FO704550.1',\n",
+ " 'name': 'NZ_FO704550.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000016425.1_ASM1642v1_genomic.fna',\n",
+ " 'description': 'NC_009380.1 Salinispora tropica CNB-440, complete genome',\n",
+ " 'id': 'NC_009380.1',\n",
+ " 'name': 'NC_009380.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_002024265.1_ASM202426v1_genomic.fna',\n",
+ " 'description': 'NZ_CP016790.1 Bacillus flexus strain KLBMP 4941 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP016790.1',\n",
+ " 'name': 'NZ_CP016790.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001447115.1_ASM144711v1_genomic.fna',\n",
+ " 'description': 'NZ_CP013222.1 Salmonella enterica subsp. enterica serovar Anatum strain GT-01, complete genome',\n",
+ " 'id': 'NZ_CP013222.1',\n",
+ " 'name': 'NZ_CP013222.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_900120345.1_PRJEB18024_genomic.fna',\n",
+ " 'description': 'NZ_LT635479.1 Eubacterium sp. Marseille-P3177 strain Marseille-P3177T genome assembly, chromosome: contig00001',\n",
+ " 'id': 'NZ_LT635479.1',\n",
+ " 'name': 'NZ_LT635479.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_002119765.1_ASM211976v1_genomic.fna',\n",
+ " 'description': 'NZ_CP021112.1 Pseudorhodoplanes sinuspersici strain RIPI110 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP021112.1',\n",
+ " 'name': 'NZ_CP021112.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_001629705.1_ASM162970v2_genomic.fna',\n",
+ " 'description': 'NZ_CP015378.1 Fictibacillus phosphorivorans strain G25-29 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP015378.1',\n",
+ " 'name': 'NZ_CP015378.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_002893885.1_ASM289388v1_genomic.fna',\n",
+ " 'description': 'NZ_CP025957.1 Paenibacillus polymyxa strain HY96-2 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP025957.1',\n",
+ " 'name': 'NZ_CP025957.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000009705.1_ASM970v1_genomic.fna',\n",
+ " 'description': 'NC_003272.1 Nostoc sp. PCC 7120 DNA, complete genome',\n",
+ " 'id': 'NC_003272.1',\n",
+ " 'name': 'NC_003272.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_000348725.1_ASM34872v1_genomic.fna',\n",
+ " 'description': 'NC_020813.1 Bdellovibrio exovorus JSS, complete genome',\n",
+ " 'id': 'NC_020813.1',\n",
+ " 'name': 'NC_020813.1'},\n",
+ " {'file': '/home/serge/development/genomes/ncbi-genomes-2019-04-07/bacterial genomes/GCF_003718655.1_ASM371865v1_genomic.fna',\n",
+ " 'description': 'NZ_CP029958.1 Salmonella enterica subsp. enterica serovar Typhi strain 311189_201186 chromosome, complete genome',\n",
+ " 'id': 'NZ_CP029958.1',\n",
+ " 'name': 'NZ_CP029958.1'},\n",
+ " ...]"
+ ]
+ },
+ "execution_count": 31,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "a"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 25,
+ "metadata": {},
+ "outputs": [
+ {
+ "ename": "AttributeError",
+ "evalue": "'list' object has no attribute 'items'",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
+ "\u001b[0;32m<ipython-input-25-cd86de522b13>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0ma\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mDataFrame\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mitems\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcolumns\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"file\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"description\"\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\"id\"\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\"name\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgroupby\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"file\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0magg\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m{\u001b[0m\u001b[0;34m\"id\"\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m'count'\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msort_values\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'id'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mascending\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+ "\u001b[0;31mAttributeError\u001b[0m: 'list' object has no attribute 'items'"
+ ]
+ }
+ ],
+ "source": [
+ "a = pd.DataFrame(data=list(a.items), columns=[\"file\", \"description\",\"id\",\"name\"]).groupby(\"file\").agg({\"id\":'count'}).sort_values('id', ascending=False)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 20,
+ "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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+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
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+ " <th>id</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>count</th>\n",
+ " <td>13050.000000</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>mean</th>\n",
+ " <td>1.956552</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>std</th>\n",
+ " <td>1.742139</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>min</th>\n",
+ " <td>1.000000</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>25%</th>\n",
+ " <td>1.000000</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>50%</th>\n",
+ " <td>1.000000</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>75%</th>\n",
+ " <td>2.000000</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>max</th>\n",
+ " <td>22.000000</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " id\n",
+ "count 13050.000000\n",
+ "mean 1.956552\n",
+ "std 1.742139\n",
+ "min 1.000000\n",
+ "25% 1.000000\n",
+ "50% 1.000000\n",
+ "75% 2.000000\n",
+ "max 22.000000"
+ ]
+ },
+ "execution_count": 20,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "a.describe()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 26,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "inventory = pd.DataFrame(data=[l.split()[1:3] for l in all_fastas], columns=[\"genus\",\"species\" ])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 30,
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
+ " .dataframe tbody tr th:only-of-type {\n",
+ " vertical-align: middle;\n",
+ " }\n",
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+ " .dataframe tbody tr th {\n",
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+ " }\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>species</th>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>genus</th>\n",
+ " <th></th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>Escherichia</th>\n",
+ " <td>2239</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Klebsiella</th>\n",
+ " <td>1718</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Salmonella</th>\n",
+ " <td>1183</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Bacillus</th>\n",
+ " <td>1172</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Lactobacillus</th>\n",
+ " <td>953</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Staphylococcus</th>\n",
+ " <td>889</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Burkholderia</th>\n",
+ " <td>650</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Enterococcus</th>\n",
+ " <td>626</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Pseudomonas</th>\n",
+ " <td>613</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Streptococcus</th>\n",
+ " <td>564</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Acinetobacter</th>\n",
+ " <td>531</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Bordetella</th>\n",
+ " <td>504</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Vibrio</th>\n",
+ " <td>474</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Xanthomonas</th>\n",
+ " <td>395</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Mycobacterium</th>\n",
+ " <td>368</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Borrelia</th>\n",
+ " <td>347</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Campylobacter</th>\n",
+ " <td>339</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Rhizobium</th>\n",
+ " <td>307</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Enterobacter</th>\n",
+ " <td>298</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Mycoplasma</th>\n",
+ " <td>290</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Corynebacterium</th>\n",
+ " <td>258</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Phaeobacter</th>\n",
+ " <td>256</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Yersinia</th>\n",
+ " <td>243</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Brucella</th>\n",
+ " <td>233</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Clostridium</th>\n",
+ " <td>228</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Listeria</th>\n",
+ " <td>227</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Streptomyces</th>\n",
+ " <td>225</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Chlamydia</th>\n",
+ " <td>202</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Helicobacter</th>\n",
+ " <td>187</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Candidatus</th>\n",
+ " <td>187</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>...</th>\n",
+ " <td>...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>'Deinococcus</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Mariniflexile</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Marinithermus</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Lactobacillales</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Marinobacterium</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Megamonas</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Melioribacter</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Melittangium</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Methylobacillus</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Methylocaldum</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Magnetococcus</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Mageeibacillus</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Lysinimonas</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Luteitalea</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Lacunisphaera</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Lautropia</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Leadbetterella</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Leminorella</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Lentibacillus</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Lentzea</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Leptothrix</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Levyella</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Limnobaculum</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Limnochorda</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Litorilituus</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Lonsdalea</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Luteibacter</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Luteipulveratus</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>secondary</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>plasmid1</th>\n",
+ " <td>0</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "<p>1120 rows × 1 columns</p>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " species\n",
+ "genus \n",
+ "Escherichia 2239\n",
+ "Klebsiella 1718\n",
+ "Salmonella 1183\n",
+ "Bacillus 1172\n",
+ "Lactobacillus 953\n",
+ "Staphylococcus 889\n",
+ "Burkholderia 650\n",
+ "Enterococcus 626\n",
+ "Pseudomonas 613\n",
+ "Streptococcus 564\n",
+ "Acinetobacter 531\n",
+ "Bordetella 504\n",
+ "Vibrio 474\n",
+ "Xanthomonas 395\n",
+ "Mycobacterium 368\n",
+ "Borrelia 347\n",
+ "Campylobacter 339\n",
+ "Rhizobium 307\n",
+ "Enterobacter 298\n",
+ "Mycoplasma 290\n",
+ "Corynebacterium 258\n",
+ "Phaeobacter 256\n",
+ "Yersinia 243\n",
+ "Brucella 233\n",
+ "Clostridium 228\n",
+ "Listeria 227\n",
+ "Streptomyces 225\n",
+ "Chlamydia 202\n",
+ "Helicobacter 187\n",
+ "Candidatus 187\n",
+ "... ...\n",
+ "'Deinococcus 1\n",
+ "Mariniflexile 1\n",
+ "Marinithermus 1\n",
+ "Lactobacillales 1\n",
+ "Marinobacterium 1\n",
+ "Megamonas 1\n",
+ "Melioribacter 1\n",
+ "Melittangium 1\n",
+ "Methylobacillus 1\n",
+ "Methylocaldum 1\n",
+ "Magnetococcus 1\n",
+ "Mageeibacillus 1\n",
+ "Lysinimonas 1\n",
+ "Luteitalea 1\n",
+ "Lacunisphaera 1\n",
+ "Lautropia 1\n",
+ "Leadbetterella 1\n",
+ "Leminorella 1\n",
+ "Lentibacillus 1\n",
+ "Lentzea 1\n",
+ "Leptothrix 1\n",
+ "Levyella 1\n",
+ "Limnobaculum 1\n",
+ "Limnochorda 1\n",
+ "Litorilituus 1\n",
+ "Lonsdalea 1\n",
+ "Luteibacter 1\n",
+ "Luteipulveratus 1\n",
+ "secondary 1\n",
+ "plasmid1 0\n",
+ "\n",
+ "[1120 rows x 1 columns]"
+ ]
+ },
+ "execution_count": 30,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "inventory.groupby(\"genus\").agg({\"species\":\"count\"}).sort_values(\"species\",ascending=False)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {},
+ "outputs": [
+ {
+ "ename": "NameError",
+ "evalue": "name 'all_fasts' is not defined",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
+ "\u001b[0;32m<ipython-input-6-6d89bdb036cc>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mall_fasts\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+ "\u001b[0;31mNameError\u001b[0m: name 'all_fasts' is not defined"
+ ]
+ }
+ ],
+ "source": [
+ "all_fasts"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 24,
+ "metadata": {
+ "scrolled": false
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
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+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
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+ " <th>count</th>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>genus</th>\n",
+ " <th>species</th>\n",
+ " <th></th>\n",
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+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>'Catharanthus</th>\n",
+ " <th>roseus'</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>'Deinococcus</th>\n",
+ " <th>soli'</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>'Nostoc</th>\n",
+ " <th>azollae'</th>\n",
+ " <td>3</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>18,711,729</th>\n",
+ " <th>reads</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Acaryochloris</th>\n",
+ " <th>marina</th>\n",
+ " <td>10</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th rowspan=\"10\" valign=\"top\">Acetobacter</th>\n",
+ " <th>aceti</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>ascendens</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>orientalis</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>oryzifermentans</th>\n",
+ " <td>1</td>\n",
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+ " <tr>\n",
+ " <th>pasteurianus</th>\n",
+ " <td>91</td>\n",
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+ " <tr>\n",
+ " <th>persici</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>pomorum</th>\n",
+ " <td>7</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>senegalensis</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>sp.</th>\n",
+ " <td>7</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>tropicalis</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Acetobacterium</th>\n",
+ " <th>woodii</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Acetohalobium</th>\n",
+ " <th>arabaticum</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Acetomicrobium</th>\n",
+ " <th>mobile</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th rowspan=\"4\" valign=\"top\">Acholeplasma</th>\n",
+ " <th>axanthum</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>hippikon</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>laidlawii</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>oculi</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th rowspan=\"5\" valign=\"top\">Achromobacter</th>\n",
+ " <th>denitrificans</th>\n",
+ " <td>3</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>insolitus</th>\n",
+ " <td>4</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>sp.</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>spanius</th>\n",
+ " <td>4</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>xylosoxidans</th>\n",
+ " <td>11</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th rowspan=\"2\" valign=\"top\">Acidaminococcus</th>\n",
+ " <th>fermentans</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>intestini</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Acidiferrobacter</th>\n",
+ " <th>sp.</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>...</th>\n",
+ " <th>...</th>\n",
+ " <td>...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Zymobacter</th>\n",
+ " <th>palmae</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Zymomonas</th>\n",
+ " <th>mobilis</th>\n",
+ " <td>49</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>[Arcobacter]</th>\n",
+ " <th>porcinus</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>[Bacillus</th>\n",
+ " <th>thuringiensis]</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th rowspan=\"2\" valign=\"top\">[Bacillus]</th>\n",
+ " <th>caldolyticus</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>selenitireducens</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th rowspan=\"2\" valign=\"top\">[Brevibacterium]</th>\n",
+ " <th>flavum</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>frigoritolerans</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th rowspan=\"8\" valign=\"top\">[Clostridium]</th>\n",
+ " <th>bolteae</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>cellulolyticum</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>cellulosi</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>clariflavum</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>propionicum</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>saccharolyticum</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>scindens</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>stercorarium</th>\n",
+ " <td>4</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>[Enterobacter]</th>\n",
+ " <th>lignolyticus</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th rowspan=\"3\" valign=\"top\">[Eubacterium]</th>\n",
+ " <th>eligens</th>\n",
+ " <td>3</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>hallii</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>rectale</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th rowspan=\"2\" valign=\"top\">[Haemophilus]</th>\n",
+ " <th>ducreyi</th>\n",
+ " <td>14</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>parasuis</th>\n",
+ " <td>4</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>[Mycobacterium]</th>\n",
+ " <th>chelonae</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>[Pasteurella]</th>\n",
+ " <th>aerogenes</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>[Polyangium]</th>\n",
+ " <th>brachysporum</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>[Pseudomonas</th>\n",
+ " <th>syringae]</th>\n",
+ " <td>3</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>[Pseudomonas]</th>\n",
+ " <th>mesoacidophila</th>\n",
+ " <td>4</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>complete</th>\n",
+ " <th>chromosome</th>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>gamma</th>\n",
+ " <th>proteobacterium</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>secondary</th>\n",
+ " <th>endosymbiont</th>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "<p>3186 rows × 1 columns</p>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " count\n",
+ "genus species \n",
+ "'Catharanthus roseus' 2\n",
+ "'Deinococcus soli' 1\n",
+ "'Nostoc azollae' 3\n",
+ "18,711,729 reads 1\n",
+ "Acaryochloris marina 10\n",
+ "Acetobacter aceti 1\n",
+ " ascendens 1\n",
+ " orientalis 2\n",
+ " oryzifermentans 1\n",
+ " pasteurianus 91\n",
+ " persici 2\n",
+ " pomorum 7\n",
+ " senegalensis 2\n",
+ " sp. 7\n",
+ " tropicalis 2\n",
+ "Acetobacterium woodii 1\n",
+ "Acetohalobium arabaticum 1\n",
+ "Acetomicrobium mobile 1\n",
+ "Acholeplasma axanthum 1\n",
+ " hippikon 2\n",
+ " laidlawii 2\n",
+ " oculi 1\n",
+ "Achromobacter denitrificans 3\n",
+ " insolitus 4\n",
+ " sp. 2\n",
+ " spanius 4\n",
+ " xylosoxidans 11\n",
+ "Acidaminococcus fermentans 1\n",
+ " intestini 1\n",
+ "Acidiferrobacter sp. 1\n",
+ "... ...\n",
+ "Zymobacter palmae 2\n",
+ "Zymomonas mobilis 49\n",
+ "[Arcobacter] porcinus 1\n",
+ "[Bacillus thuringiensis] 2\n",
+ "[Bacillus] caldolyticus 2\n",
+ " selenitireducens 1\n",
+ "[Brevibacterium] flavum 2\n",
+ " frigoritolerans 1\n",
+ "[Clostridium] bolteae 2\n",
+ " cellulolyticum 1\n",
+ " cellulosi 1\n",
+ " clariflavum 1\n",
+ " propionicum 1\n",
+ " saccharolyticum 1\n",
+ " scindens 1\n",
+ " stercorarium 4\n",
+ "[Enterobacter] lignolyticus 1\n",
+ "[Eubacterium] eligens 3\n",
+ " hallii 1\n",
+ " rectale 1\n",
+ "[Haemophilus] ducreyi 14\n",
+ " parasuis 4\n",
+ "[Mycobacterium] chelonae 2\n",
+ "[Pasteurella] aerogenes 1\n",
+ "[Polyangium] brachysporum 1\n",
+ "[Pseudomonas syringae] 3\n",
+ "[Pseudomonas] mesoacidophila 4\n",
+ "complete chromosome 2\n",
+ "gamma proteobacterium 1\n",
+ "secondary endosymbiont 1\n",
+ "\n",
+ "[3186 rows x 1 columns]"
+ ]
+ },
+ "execution_count": 24,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "inventory.groupby([\"genus\", \"species\"]).agg({\"species\": \"count\"})\n",
+ "inventory.columns=[\"count\"]\n",
+ "inventory"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 25,
+ "metadata": {
+ "collapsed": true
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "['NZ_CP013305.1 Vibrio cholerae strain CRC1106 chromosome 1, complete sequence',\n",
+ " 'NZ_CP013306.1 Vibrio cholerae strain CRC1106 chromosome 2, complete sequence',\n",
+ " 'NC_013791.2 Bacillus pseudofirmus OF4, complete genome',\n",
+ " 'NC_013792.1 Bacillus pseudofirmus OF4 plasmid pBpOF4-01, complete sequence',\n",
+ " 'NC_013793.1 Bacillus pseudofirmus OF4 plasmid pBpOF4-02, complete sequence',\n",
+ " 'NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome',\n",
+ " 'NC_007164.1 Corynebacterium jeikeium K411 complete genome',\n",
+ " 'NC_003080.1 Corynebacterium jeikeium K411 plasmid pKW4, complete sequence',\n",
+ " 'NC_002162.1 Ureaplasma parvum serovar 3 str. ATCC 700970, complete genome',\n",
+ " 'NC_004088.1 Yersinia pestis KIM10+, complete genome',\n",
+ " 'NC_004838.1 Yersinia pestis KIM10+ plasmid pMT-1, complete sequence',\n",
+ " 'NC_002620.2 Chlamydia muridarum Nigg, complete genome',\n",
+ " 'NC_002182.1 Chlamydia muridarum Nigg plasmid pMoPn, complete sequence',\n",
+ " 'NC_002488.3 Xylella fastidiosa 9a5c, complete genome',\n",
+ " 'NC_002489.3 Xylella fastidiosa 9a5c plasmid pXF1.3, complete sequence',\n",
+ " 'NC_002490.1 Xylella fastidiosa 9a5c plasmid pXF51, complete sequence',\n",
+ " 'NC_002505.1 Vibrio cholerae O1 biovar El Tor str. N16961 chromosome I, complete sequence',\n",
+ " 'NC_002506.1 Vibrio cholerae O1 biovar El Tor str. N16961 chromosome II, complete sequence',\n",
+ " 'NC_002516.2 Pseudomonas aeruginosa PAO1, complete genome',\n",
+ " 'NC_002737.2 Streptococcus pyogenes M1 GAS, complete genome',\n",
+ " 'NC_002663.1 Pasteurella multocida subsp. multocida str. Pm70, complete genome',\n",
+ " 'NC_002946.2 Neisseria gonorrhoeae FA 1090 chromosome, complete genome',\n",
+ " 'NC_002662.1 Lactococcus lactis subsp. lactis Il1403 chromosome, complete genome',\n",
+ " 'NC_003028.3 Streptococcus pneumoniae TIGR4, complete genome',\n",
+ " 'NC_002696.2 Caulobacter crescentus CB15 chromosome, complete genome',\n",
+ " 'NC_004337.2 Shigella flexneri 2a str. 301 chromosome, complete genome',\n",
+ " 'NC_004851.1 Shigella flexneri 2a str. 301 plasmid pCP301, complete sequence',\n",
+ " 'NC_013174.1 Jonesia denitrificans DSM 20603, complete genome',\n",
+ " 'NC_013166.1 Kangiella koreensis DSM 16069, complete genome',\n",
+ " 'NC_013171.1 Anaerococcus prevotii DSM 20548, complete genome',\n",
+ " 'NC_013164.1 Anaerococcus prevotii DSM 20548 plasmid pAPRE01, complete sequence',\n",
+ " 'NC_013222.1 Robiginitalea biformata HTCC2501, complete genome',\n",
+ " 'NC_017285.1 Chlamydophila pneumoniae LPCoLN, complete genome',\n",
+ " 'NC_017286.1 Chlamydophila pneumoniae LPCoLN plasmid, complete sequence',\n",
+ " 'NC_013194.1 Candidatus Accumulibacter phosphatis clade IIA str. UW-1, complete genome',\n",
+ " 'NC_013193.1 Candidatus Accumulibacter phosphatis clade IIA str. UW-1 plasmid pAph01, complete sequence',\n",
+ " 'NC_013190.1 Candidatus Accumulibacter phosphatis clade IIA str. UW-1 plasmid pAph02, complete sequence',\n",
+ " 'NC_013191.1 Candidatus Accumulibacter phosphatis clade IIA str. UW-1 plasmid pAph03, complete sequence',\n",
+ " 'NC_013216.1 Desulfotomaculum acetoxidans DSM 771, complete genome',\n",
+ " 'NC_013203.1 Atopobium parvulum DSM 20469, complete genome',\n",
+ " 'NC_013355.1 Zymomonas mobilis subsp. mobilis NCIMB 11163, complete genome',\n",
+ " 'NC_013356.1 Zymomonas mobilis subsp. mobilis NCIMB 11163 plasmid pZA1001, complete sequence',\n",
+ " 'NC_013357.1 Zymomonas mobilis subsp. mobilis NCIMB 11163 plasmid pZA1002, complete sequence',\n",
+ " 'NC_013358.1 Zymomonas mobilis subsp. mobilis NCIMB 11163 plasmid pZA1003, complete sequence',\n",
+ " 'NC_013204.1 Eggerthella lenta DSM 2243, complete genome',\n",
+ " 'NC_013205.1 Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446, complete genome',\n",
+ " 'NC_013206.1 Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 plasmid pAACI01, complete sequence',\n",
+ " 'NC_013207.1 Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 plasmid pAACI02, complete sequence',\n",
+ " 'NC_013208.1 Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 plasmid pAACI03, complete sequence',\n",
+ " 'NC_013223.1 Desulfohalobium retbaense DSM 5692, complete genome',\n",
+ " 'NC_013224.1 Desulfohalobium retbaense DSM 5692 plasmid pDRET01, complete sequence',\n",
+ " 'NC_009883.1 Rickettsia bellii OSU 85-389, complete genome',\n",
+ " 'NC_009953.1 Salinispora arenicola CNS-205, complete genome',\n",
+ " 'NC_009901.1 Shewanella pealeana ATCC 700345, complete genome',\n",
+ " 'NC_009922.1 Alkaliphilus oremlandii OhILAs, complete genome',\n",
+ " 'NC_010612.1 Mycobacterium marinum M, complete genome',\n",
+ " 'NC_010604.1 Mycobacterium marinum M plasmid pMM23, complete sequence',\n",
+ " 'NC_012125.1 Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594, complete genome',\n",
+ " 'NC_012124.1 Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594 plasmid pSPCV, complete sequence',\n",
+ " 'NC_009943.1 Desulfococcus oleovorans Hxd3, complete genome',\n",
+ " 'NC_010424.1 Candidatus Desulforudis audaxviator MP104C, complete genome',\n",
+ " 'NC_010611.1 Acinetobacter baumannii ACICU, complete genome',\n",
+ " 'NC_010605.1 Acinetobacter baumannii ACICU plasmid pACICU1, complete sequence',\n",
+ " 'NC_010606.1 Acinetobacter baumannii ACICU plasmid pACICU2, complete sequence',\n",
+ " 'NC_010084.1 Burkholderia multivorans ATCC 17616 chromosome 1, complete sequence',\n",
+ " 'NC_010086.1 Burkholderia multivorans ATCC 17616 chromosome 2, complete sequence',\n",
+ " 'NC_010087.1 Burkholderia multivorans ATCC 17616 chromosome 3, complete sequence',\n",
+ " 'NC_010070.1 Burkholderia multivorans ATCC 17616 plasmid pBMUL01, complete sequence',\n",
+ " 'NC_010103.1 Brucella canis ATCC 23365 chromosome I, complete sequence',\n",
+ " 'NC_010104.1 Brucella canis ATCC 23365 chromosome II, complete sequence',\n",
+ " 'NC_012587.1 Sinorhizobium fredii NGR234 chromosome, complete genome',\n",
+ " 'NC_000914.2 Sinorhizobium fredii NGR234 plasmid pNGR234a, complete sequence',\n",
+ " 'NC_012586.1 Sinorhizobium fredii NGR234 plasmid pNGR234b, complete sequence',\n",
+ " 'NC_010003.1 Petrotoga mobilis SJ95, complete genome',\n",
+ " 'NC_010067.1 Salmonella enterica subsp. arizonae serovar 62:z4,z23:--, complete genome',\n",
+ " 'NC_010002.1 Delftia acidovorans SPH-1, complete genome',\n",
+ " 'NC_010001.1 Lachnoclostridium phytofermentans ISDg, complete genome',\n",
+ " 'NC_010102.1 Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7, complete genome',\n",
+ " 'NC_010742.1 Brucella abortus S19 chromosome 1, complete sequence',\n",
+ " 'NC_010740.1 Brucella abortus S19 chromosome 2, complete sequence',\n",
+ " 'NC_010117.1 Coxiella burnetii RSA 331, complete genome',\n",
+ " 'NC_010115.1 Coxiella burnetii RSA 331 plasmid QpH1, complete sequence',\n",
+ " 'NC_009997.1 Shewanella baltica OS195, complete genome',\n",
+ " 'NC_009998.1 Shewanella baltica OS195 plasmid pS19501, complete sequence',\n",
+ " 'NC_009999.1 Shewanella baltica OS195 plasmid pS19502, complete sequence',\n",
+ " 'NC_010000.1 Shewanella baltica OS195 plasmid pS19503, complete sequence',\n",
+ " 'NC_010163.1 Acholeplasma laidlawii PG-8A, complete genome',\n",
+ " 'NC_003197.2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, complete genome',\n",
+ " 'NC_003277.2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 plasmid pSLT, complete sequence',\n",
+ " 'NC_004631.1 Salmonella enterica subsp. enterica serovar Typhi Ty2, complete genome',\n",
+ " 'NC_002944.2 Mycobacterium avium subsp. paratuberculosis str. k10, complete genome',\n",
+ " 'NC_007332.1 Mycoplasma hyopneumoniae 7448, complete genome',\n",
+ " 'NC_005957.1 [Bacillus thuringiensis] serovar konkukian str. 97-27 chromosome, complete genome',\n",
+ " 'NC_006578.1 [Bacillus thuringiensis] serovar konkukian str. 97-27 plasmid pBT9727, complete sequence',\n",
+ " 'NC_010816.1 Bifidobacterium longum DJO10A, complete genome',\n",
+ " 'NC_004252.1 Bifidobacterium longum DJO10A plasmid pDOJH10L, complete sequence',\n",
+ " 'NC_004253.1 Bifidobacterium longum DJO10A plasmid pDOJH10S, complete sequence',\n",
+ " 'NC_008800.1 Yersinia enterocolitica subsp. enterocolitica 8081 chromosome, complete genome',\n",
+ " 'NC_008791.1 Yersinia enterocolitica subsp. enterocolitica 8081 plasmid pYVe8081, complete sequence',\n",
+ " 'NC_003272.1 Nostoc sp. PCC 7120 DNA, complete genome',\n",
+ " 'NC_003276.1 Nostoc sp. PCC 7120 plasmid pCC7120alpha DNA, complete genome',\n",
+ " 'NC_003240.1 Nostoc sp. PCC 7120 plasmid pCC7120beta DNA, complete sequence',\n",
+ " 'NC_003273.1 Nostoc sp. PCC 7120 plasmid pCC7120delta DNA, complete sequence',\n",
+ " 'NC_003270.1 Nostoc sp. PCC 7120 plasmid pCC7120epsilon DNA, complete sequence',\n",
+ " 'NC_003267.1 Nostoc sp. PCC 7120 plasmid pCC7120gamma DNA, complete sequence',\n",
+ " 'NC_003241.1 Nostoc sp. PCC 7120 plasmid pCC7120zeta DNA, complete sequence',\n",
+ " 'NC_009342.1 Corynebacterium glutamicum R DNA, complete genome',\n",
+ " 'NC_009343.1 Corynebacterium glutamicum R plasmid pCGR1 DNA, complete sequence',\n",
+ " 'NC_010729.1 Porphyromonas gingivalis ATCC 33277 DNA, complete genome',\n",
+ " 'NC_013799.1 Hydrogenobacter thermophilus TK-6 DNA, complete genome',\n",
+ " 'NC_003450.3 Corynebacterium glutamicum ATCC 13032 chromosome, complete genome',\n",
+ " 'NC_017382.1 Helicobacter pylori 51, complete genome',\n",
+ " 'NC_008322.1 Shewanella sp. MR-7, complete genome',\n",
+ " 'NC_008320.1 Shewanella sp. MR-7, complete sequence',\n",
+ " 'NC_008321.1 Shewanella sp. MR-4, complete genome',\n",
+ " 'NC_008345.1 Shewanella frigidimarina NCIMB 400, complete genome',\n",
+ " 'NC_008346.1 Syntrophomonas wolfei subsp. wolfei str. Goettingen G311, complete genome',\n",
+ " 'NC_008347.1 Maricaulis maris MCS10, complete genome',\n",
+ " 'NC_008344.1 Nitrosomonas eutropha C91, complete genome',\n",
+ " 'NC_008341.1 Nitrosomonas eutropha C91 Plasmid1, complete sequence',\n",
+ " 'NC_008342.1 Nitrosomonas eutropha C91 Plasmid2, complete sequence',\n",
+ " 'NC_008340.1 Alkalilimnicola ehrlichii MLHE-1, complete genome',\n",
+ " 'NC_008570.1 Aeromonas hydrophila subsp. hydrophila ATCC 7966 chromosome, complete genome',\n",
+ " 'NC_008435.1 Rhodopseudomonas palustris BisA53, complete genome',\n",
+ " 'NC_008563.1 Escherichia coli APEC O1, complete genome',\n",
+ " 'NC_009837.1 Escherichia coli APEC O1 plasmid pAPEC-O1-ColBM, complete sequence',\n",
+ " 'NC_009838.1 Escherichia coli APEC O1 plasmid pAPEC-O1-R, complete sequence',\n",
+ " 'NC_008576.1 Magnetococcus marinus MC-1, complete genome',\n",
+ " 'NC_011566.1 Shewanella piezotolerans WP3, complete genome',\n",
+ " 'NC_008536.1 Candidatus Solibacter usitatus Ellin6076, complete genome',\n",
+ " 'NC_008711.1 Paenarthrobacter aurescens TC1, complete genome',\n",
+ " 'NC_008712.1 Paenarthrobacter aurescens TC1 plasmid TC1, complete sequence',\n",
+ " 'NC_008713.1 Paenarthrobacter aurescens TC1 plasmid TC2, complete sequence',\n",
+ " 'NC_008554.1 Syntrophobacter fumaroxidans MPOB, complete genome',\n",
+ " 'NC_008595.1 Mycobacterium avium 104, complete genome',\n",
+ " 'NC_008596.1 Mycobacterium smegmatis str. MC2 155 chromosome, complete genome',\n",
+ " 'NC_008578.1 Acidothermus cellulolyticus 11B, complete genome',\n",
+ " 'NC_008609.1 Pelobacter propionicus DSM 2379, complete genome',\n",
+ " 'NC_008607.1 Pelobacter propionicus DSM 2379 plasmid pPRO1, complete sequence',\n",
+ " 'NC_008608.1 Pelobacter propionicus DSM 2379 plasmid pPRO2, complete sequence',\n",
+ " 'NC_008600.1 Bacillus thuringiensis str. Al Hakam, complete genome',\n",
+ " 'NC_008598.1 Bacillus thuringiensis str. Al Hakam, plasmid pALH1, complete sequence',\n",
+ " 'NC_013928.1 Streptococcus mutans NN2025 DNA, complete genome',\n",
+ " 'NC_014215.1 Propionibacterium freudenreichii subsp. shermanii CIRM-BIA1, complete genome',\n",
+ " 'NC_013861.1 Legionella longbeachae NSW150, complete genome',\n",
+ " 'NC_014544.1 Legionella longbeachae NSW150 plasmid pLLO',\n",
+ " 'NC_012925.1 Streptococcus suis P1/7 complete genome',\n",
+ " 'NC_013949.1 Helicobacter mustelae 12198 complete genome',\n",
+ " 'NC_003062.2 Agrobacterium fabrum str. C58 chromosome circular, complete sequence',\n",
+ " 'NC_003063.2 Agrobacterium fabrum str. C58 chromosome linear, complete sequence',\n",
+ " 'NC_003064.2 Agrobacterium fabrum str. C58 plasmid At, complete sequence',\n",
+ " 'NC_003065.3 Agrobacterium fabrum str. C58 plasmid Ti, complete sequence',\n",
+ " 'NC_007761.1 Rhizobium etli CFN 42, complete genome',\n",
+ " 'NC_007762.1 Rhizobium etli CFN 42 plasmid p42a, complete sequence',\n",
+ " 'NC_007763.1 Rhizobium etli CFN 42 plasmid p42b, complete sequence',\n",
+ " 'NC_007764.1 Rhizobium etli CFN 42 plasmid p42c, complete sequence',\n",
+ " 'NC_007765.1 Rhizobium etli CFN 42 plasmid p42e, complete sequence',\n",
+ " 'NC_007766.1 Rhizobium etli CFN 42 plasmid p42f, complete sequence',\n",
+ " 'NC_004041.2 Rhizobium etli CFN 42 plasmid symbiotic plasmid p42d, complete sequence',\n",
+ " 'NC_014148.1 Planctopirus limnophila DSM 3776, complete genome',\n",
+ " 'NC_014149.1 Planctopirus limnophila DSM 3776 plasmid pPLIM01, complete sequence',\n",
+ " 'NC_014212.1 Meiothermus silvanus DSM 9946, complete genome',\n",
+ " 'NC_014213.1 Meiothermus silvanus DSM 9946 plasmid pMESIL01, complete sequence',\n",
+ " 'NC_014214.1 Meiothermus silvanus DSM 9946 plasmid pMESIL02, complete sequence',\n",
+ " 'NC_014171.1 Bacillus thuringiensis BMB171, complete genome',\n",
+ " 'NC_014172.1 Bacillus thuringiensis BMB171 plasmid pBMB171, complete sequence',\n",
+ " 'NC_014216.1 Desulfurivibrio alkaliphilus AHT2, complete genome',\n",
+ " 'NC_014158.1 Tsukamurella paurometabola DSM 20162, complete genome',\n",
+ " 'NC_014159.1 Tsukamurella paurometabola DSM 20162 plasmid pTpau01, complete sequence',\n",
+ " 'NC_014166.1 Arcobacter nitrofigilis DSM 7299, complete genome',\n",
+ " 'NC_014147.1 Moraxella catarrhalis BBH18, complete genome',\n",
+ " 'NC_014100.1 Caulobacter segnis ATCC 21756, complete genome',\n",
+ " 'NC_014169.1 Bifidobacterium longum subsp. longum JDM301, complete genome',\n",
+ " 'NC_017297.1 Clostridium botulinum F str. 230613, complete genome',\n",
+ " 'NC_017298.1 Clostridium botulinum F str. 230613 plasmid pCBF, complete sequence',\n",
+ " 'NC_014218.1 Arcanobacterium haemolyticum DSM 20595, complete genome',\n",
+ " 'NC_016582.1 Streptomyces bingchenggensis BCW-1, complete genome',\n",
+ " 'NC_014220.1 Syntrophothermus lipocalidus DSM 12680, complete genome',\n",
+ " 'NC_017633.1 Escherichia coli ETEC H10407, complete genome',\n",
+ " 'NC_017721.1 Escherichia coli ETEC H10407 p52 plasmid',\n",
+ " 'NC_017723.1 Escherichia coli ETEC H10407 p58 plasmid',\n",
+ " 'NC_017722.1 Escherichia coli ETEC H10407 p666 plasmid',\n",
+ " 'NC_017724.1 Escherichia coli ETEC H10407 p948 plasmid',\n",
+ " 'NC_017441.1 Chlamydia trachomatis Sweden2, complete genome',\n",
+ " 'NC_017465.1 Lactobacillus fermentum CECT 5716, complete genome',\n",
+ " 'NC_018588.1 Listeria monocytogenes strain SLCC2372, serotype 1/2c',\n",
+ " 'NC_018889.1 Listeria monocytogenes serotype 1-2c str. SLCC2372 plasmid pLM1-2cUG1 complete sequence',\n",
+ " 'NC_016776.1 Bacteroides fragilis 638R genome',\n",
+ " 'NC_016810.1 Salmonella enterica subsp. enterica serovar Typhimurium SL1344 complete genome',\n",
+ " 'NC_017718.1 Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 plasmid pCol1B9_SL1344 complete sequence',\n",
+ " 'NC_017719.1 Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 plasmid pRSF1010_SL1344 complete sequence',\n",
+ " 'NC_017720.1 Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 plasmid pSLT_SL1344 complete sequence',\n",
+ " 'NC_016809.1 Haemophilus influenzae 10810 genome',\n",
+ " 'NC_015964.1 Haemophilus parainfluenzae T3T1 complete genome',\n",
+ " 'NC_016620.1 Bacteriovorax marinus SJ genome',\n",
+ " 'NC_019100.1 Bacteriovorax marinus SJ plasmid pBMS1 complete sequence',\n",
+ " 'NC_017593.1 Streptococcus pneumoniae INV200 genome',\n",
+ " 'NC_017592.1 Streptococcus pneumoniae OXC141 complete genome',\n",
+ " 'NC_017591.1 Streptococcus pneumoniae INV104 genome',\n",
+ " 'NC_021006.1 Streptococcus pneumoniae SPN034156 draft genome',\n",
+ " 'NC_021028.1 Streptococcus pneumoniae SPN034183 draft genome',\n",
+ " 'NC_021026.1 Streptococcus pneumoniae SPN994038 draft genome',\n",
+ " 'NC_021005.1 Streptococcus pneumoniae SPN994039 draft genome',\n",
+ " 'NC_021003.1 Streptococcus pneumoniae SPN032672 draft genome',\n",
+ " 'NC_021004.1 Streptococcus pneumoniae SPN033038 draft genome',\n",
+ " 'NC_017519.1 Mycoplasma hyorhinis MCLD, complete genome',\n",
+ " 'NC_015428.1 Lactobacillus buchneri NRRL B-30929, complete genome',\n",
+ " 'NC_015420.1 Lactobacillus buchneri NRRL B-30929 plasmid pLBUC01, complete sequence',\n",
+ " 'NC_015429.1 Lactobacillus buchneri NRRL B-30929 plasmid pLBUC02, complete sequence',\n",
+ " 'NC_015421.1 Lactobacillus buchneri NRRL B-30929 plasmid pLBUC03, complete sequence',\n",
+ " 'NC_023030.2 Mycoplasma gallisepticum S6, complete genome',\n",
+ " 'NC_015638.1 Lacinutrix sp. 5H-3-7-4, complete genome',\n",
+ " 'NC_015497.1 Glaciecola sp. 4H-3-7+YE-5, complete genome',\n",
+ " 'NC_015498.1 Glaciecola sp. 4H-3-7+YE-5 plasmid pGLAAG01, complete sequence',\n",
+ " 'NC_015496.1 Dokdonia sp. 4H-3-7-5, complete genome',\n",
+ " 'NC_015501.1 Porphyromonas asaccharolytica DSM 20707, complete genome',\n",
+ " 'NC_018080.1 Pseudomonas aeruginosa DK2, complete genome',\n",
+ " 'NC_018081.1 Enterococcus hirae ATCC 9790, complete genome',\n",
+ " 'NC_015845.1 Enterococcus hirae ATCC 9790 plasmid pTG9790, complete sequence',\n",
+ " 'NZ_CP010978.1 Pelosinus fermentans JBW45, complete genome',\n",
+ " 'NC_018089.1 Streptococcus mutans GS-5, complete genome',\n",
+ " 'NZ_CP015923.1 Salmonella enterica subsp. enterica serovar Newport str. Levine 1, complete genome',\n",
+ " 'NZ_CP015924.1 Salmonella enterica subsp. enterica serovar Newport str. Levine 15, complete genome',\n",
+ " 'NZ_CP015876.1 Pseudomonas putida SJTE-1, complete genome',\n",
+ " 'NZ_CP015877.1 Pseudomonas aeruginosa SJTD-1, complete genome',\n",
+ " 'NZ_CP010283.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 21550, complete genome',\n",
+ " 'NZ_CP009564.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 21550 plasmid pCVM21550, complete sequence',\n",
+ " 'NZ_CP010281.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 22513, complete genome',\n",
+ " 'NZ_CP009562.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 22513 plasmid pCVM22513, complete sequence',\n",
+ " 'NZ_CP010282.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 21538, complete genome',\n",
+ " 'NZ_CP009563.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 21538 plasmid pCVM21538, complete sequence',\n",
+ " 'NZ_CP010279.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 22425, complete genome',\n",
+ " 'NZ_CP009560.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 22425 plasmid pCVM22425, complete sequence',\n",
+ " 'NZ_CP009561.1 Salmonella enterica subsp. enterica serovar Newport str. CVM N18486, complete genome',\n",
+ " 'NZ_CP010284.1 Salmonella enterica subsp. enterica serovar Newport str. CVM N1543, complete genome',\n",
+ " 'NZ_CP009570.1 Salmonella enterica subsp. enterica serovar Newport str. CVM N1543 plasmid pCVMN1543, complete sequence',\n",
+ " 'NZ_CP010280.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 22462, complete genome',\n",
+ " 'NZ_CP009567.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 22462 plasmid pCFSAN000934_02, complete sequence',\n",
+ " 'NZ_CP009568.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 22462 plasmid pCFSAN000934_03, complete sequence',\n",
+ " 'NZ_CP009566.1 Salmonella enterica subsp. enterica serovar Newport str. CVM 22462 plasmid pCVM22462, complete sequence',\n",
+ " 'NC_018108.1 Taylorella equigenitalis ATCC 35865, complete genome',\n",
+ " 'NC_018106.1 Klebsiella michiganensis E718, complete sequence',\n",
+ " 'NC_021501.1 Klebsiella michiganensis strain E718 plasmid pKOX_NDM1, complete sequence',\n",
+ " 'NC_018107.1 Klebsiella michiganensis E718 plasmid pKOX_R1, complete sequence',\n",
+ " 'NC_016948.1 Mycobacterium intracellulare MOTT-64, complete genome',\n",
+ " 'NC_016946.1 Mycobacterium intracellulare ATCC 13950, complete genome',\n",
+ " 'NC_016947.1 Mycobacterium intracellulare MOTT-02, complete genome',\n",
+ " 'NC_017049.1 Rickettsia prowazekii str. Chernikova, complete genome',\n",
+ " 'NZ_CP007066.1 Fusobacterium nucleatum subsp. vincentii 3_1_27 plasmid, complete sequence',\n",
+ " 'NZ_CP007064.1 Fusobacterium nucleatum subsp. vincentii 3_1_27 chromosome 1, complete sequence',\n",
+ " 'NZ_CP007065.1 Fusobacterium nucleatum subsp. vincentii 3_1_27 chromosome 2, complete sequence',\n",
+ " 'NZ_CP008742.1 Pseudomonas savastanoi pv. savastanoi NCPPB 3335, complete genome',\n",
+ " 'NC_015678.1 Streptococcus parasanguinis ATCC 15912, complete genome',\n",
+ " 'NC_014643.1 Rothia dentocariosa ATCC 17931, complete genome',\n",
+ " 'NC_014618.1 Enterobacter lignolyticus SCF1, complete genome',\n",
+ " 'NC_014625.1 Ketogulonicigenium vulgare Y25, complete genome',\n",
+ " 'NC_014621.1 Ketogulonicigenium vulgare Y25 plasmid pYP1, complete sequence',\n",
+ " 'NC_014626.1 Ketogulonicigenium vulgare Y25 plasmid pYP12, complete sequence',\n",
+ " 'NC_017161.1 Hydrogenobacter thermophilus TK-6, complete genome',\n",
+ " 'NC_014616.1 Bifidobacterium bifidum S17, complete genome',\n",
+ " 'NC_014622.2 Paenibacillus polymyxa SC2, complete genome',\n",
+ " 'NC_014628.2 Paenibacillus polymyxa SC2 plasmid pSC2, complete sequence',\n",
+ " 'NC_017455.1 Halanaerobium praevalens DSM 2228, complete genome',\n",
+ " 'NC_014623.1 Stigmatella aurantiaca DW4/3-1, complete genome',\n",
+ " 'NC_014632.1 Ilyobacter polytropus DSM 2926, complete genome',\n",
+ " 'NC_014633.1 Ilyobacter polytropus DSM 2926 plasmid pILYOP01, complete sequence',\n",
+ " 'NC_014634.1 Ilyobacter polytropus DSM 2926 plasmid pILYOP02, complete sequence',\n",
+ " 'NC_017451.1 Haemophilus influenzae R2866, complete genome',\n",
+ " 'NC_017452.1 Haemophilus influenzae R2846, complete genome',\n",
+ " 'NC_015174.1 Rubinisphaera brasiliensis DSM 5305, complete genome',\n",
+ " 'NC_015214.1 Lactobacillus amylovorus strain 30SC, complete genome',\n",
+ " 'NC_015213.1 Lactobacillus amylovorus strain 30SC plasmid pRKC30SC1, complete sequence',\n",
+ " 'NC_015218.1 Lactobacillus amylovorus strain 30SC plasmid pRKC30SC2, complete sequence',\n",
+ " 'NC_017569.1 Riemerella anatipestifer RA-GD, complete genome',\n",
+ " 'NC_017295.1 Clostridium acetobutylicum EA 2018, complete genome',\n",
+ " 'NC_017296.1 Clostridium acetobutylicum EA 2018 EA2018plasmid, complete sequence',\n",
+ " 'NC_015470.1 Chlamydia psittaci 6BC, complete genome',\n",
+ " 'NC_015217.1 Chlamydia psittaci 6BC plasmid p6BC, complete sequence',\n",
+ " 'NZ_CP019725.1 Xanthomonas perforans 91-118 chromosome, complete genome',\n",
+ " 'NC_015224.1 Yersinia enterocolitica subsp. palearctica 105.5R(r), complete genome',\n",
+ " 'NC_015475.1 Yersinia enterocolitica subsp. palearctica 105.5R(r) plasmid 105.5R(r)p, complete sequence',\n",
+ " 'NC_017374.1 Helicobacter pylori 2017, complete genome',\n",
+ " 'NC_017381.1 Helicobacter pylori 2018, complete genome',\n",
+ " 'NZ_CP017125.1 Mycoplasma capricolum subsp. capripneumoniae M1601 chromosome, complete genome',\n",
+ " 'NC_015508.1 Agrobacterium sp. H13-3 linear chromosome, complete sequence',\n",
+ " 'NC_015183.1 Agrobacterium sp. H13-3 circular chromosome, complete sequence',\n",
+ " 'NC_015184.1 Agrobacterium sp. H13-3 plasmid pAspH13-3a, complete sequence',\n",
+ " 'NC_017486.1 Lactococcus lactis subsp. lactis CV56, complete genome',\n",
+ " 'NC_017483.1 Lactococcus lactis subsp. lactis CV56 plasmid pCV56A, complete sequence',\n",
+ " 'NC_017487.1 Lactococcus lactis subsp. lactis CV56 plasmid pCV56B, complete sequence',\n",
+ " 'NC_017484.1 Lactococcus lactis subsp. lactis CV56 plasmid pCV56C, complete sequence',\n",
+ " 'NC_017485.1 Lactococcus lactis subsp. lactis CV56 plasmid pCV56D, complete sequence',\n",
+ " 'NC_017488.1 Lactococcus lactis subsp. lactis CV56 plasmid pCV56E, complete sequence',\n",
+ " 'NC_017244.1 Brucella melitensis M28 chromosome 1, complete sequence',\n",
+ " 'NC_017245.1 Brucella melitensis M28 chromosome 2, complete sequence',\n",
+ " 'NC_015259.1 Polymorphum gilvum SL003B-26A1, complete genome',\n",
+ " 'NC_015258.1 Polymorphum gilvum SL003B-26A1 plasmid pSL003B, complete sequence',\n",
+ " 'NC_015277.1 Sphingobacterium sp. 21, complete genome',\n",
+ " 'NC_016783.1 Corynebacterium diphtheriae INCA 402, complete genome',\n",
+ " 'NC_016800.1 Corynebacterium diphtheriae BH8, complete genome',\n",
+ " 'NC_017033.1 Frateuria aurantia DSM 6220, complete genome',\n",
+ " 'NC_019960.1 Prevotella dentalis DSM 3688 chromosome 1, complete sequence',\n",
+ " 'NC_019968.1 Prevotella dentalis DSM 3688 chromosome 2, complete sequence',\n",
+ " 'NC_019961.1 Prevotella dentalis DSM 3688 plasmid pPREDE01, complete sequence',\n",
+ " 'NC_019969.1 Prevotella dentalis DSM 3688 plasmid pPREDE02, complete sequence',\n",
+ " 'NC_019892.1 Singulisphaera acidiphila DSM 18658, complete genome',\n",
+ " 'NC_019893.1 Singulisphaera acidiphila DSM 18658 plasmid pSINAC01, complete sequence',\n",
+ " 'NC_019894.1 Singulisphaera acidiphila DSM 18658 plasmid pSINAC02, complete sequence',\n",
+ " 'NC_019895.1 Singulisphaera acidiphila DSM 18658 plasmid pSINAC03, complete sequence',\n",
+ " 'NC_017098.1 Spirochaeta africana DSM 8902, complete genome',\n",
+ " 'NC_017770.1 Solitalea canadensis DSM 3403, complete genome',\n",
+ " 'NC_016787.1 Corynebacterium diphtheriae HC03, complete genome',\n",
+ " 'NC_020272.1 Bacillus amyloliquefaciens IT-45, complete genome',\n",
+ " 'NC_020273.1 Bacillus amyloliquefaciens IT-45 plasmid pBA45-1, whole genome shotgun sequence',\n",
+ " 'NC_021171.1 Bacillus sp. 1NLA3E, complete genome',\n",
+ " 'NZ_CP007053.1 Opitutaceae bacterium TAV5, complete genome',\n",
+ " 'NZ_CP007054.1 Opitutaceae bacterium TAV5 plasmid, complete sequence',\n",
+ " 'NC_016745.1 Oceanimonas sp. GK1, complete genome',\n",
+ " 'NC_016746.1 Oceanimonas sp. GK1 plasmid pOCEGK01, complete sequence',\n",
+ " 'NC_016747.1 Oceanimonas sp. GK1 plasmid pOCEGK02, complete sequence',\n",
+ " 'NZ_CP007035.1 Niabella soli DSM 19437, complete genome',\n",
+ " 'NC_019903.1 Desulfitobacterium dichloroeliminans LMG P-21439, complete genome',\n",
+ " 'NC_018017.1 Desulfitobacterium dehalogenans ATCC 51507, complete genome',\n",
+ " 'NC_016791.1 Clostridium sp. BNL1100, complete genome',\n",
+ " 'NZ_CP006932.1 Candidatus Hepatoplasma crinochetorum Av, complete genome',\n",
+ " 'NZ_CP006829.1 Thalassolituus oleivorans R6-15, complete genome',\n",
+ " 'NZ_CP007122.1 Lactobacillus paracasei N1115, complete genome',\n",
+ " 'NZ_CP007123.1 Lactobacillus paracasei N1115 plasmid, complete sequence',\n",
+ " 'NZ_CP007124.1 Lactobacillus paracasei N1115 plasmid, complete sequence',\n",
+ " 'NZ_CP007125.1 Lactobacillus paracasei N1115 plasmid, complete sequence',\n",
+ " 'NZ_CP007126.1 Lactobacillus paracasei N1115 plasmid, complete sequence',\n",
+ " 'NC_022568.1 Listeria monocytogenes EGD, complete genome',\n",
+ " 'NZ_CP007244.1 Bacillus amyloliquefaciens subsp. plantarum TrigoCor1448, complete genome',\n",
+ " 'NZ_CP006742.1 Bacillus anthracis str. SVA11, complete genome',\n",
+ " 'NZ_CP006743.1 Bacillus anthracis str. SVA11 plasmid pXO1, complete sequence',\n",
+ " 'NZ_CP006744.1 Bacillus anthracis str. SVA11 plasmid pXO2, complete sequence',\n",
+ " 'NZ_CP007183.1 Campylobacter coli RM1875, complete genome',\n",
+ " 'NZ_CP007185.1 Campylobacter coli RM1875 plasmid pRM1875_2.4kb, complete sequence',\n",
+ " 'NZ_CP007186.1 Campylobacter coli RM1875 plasmid pRM1875_3.3kb, complete sequence',\n",
+ " 'NZ_CP007187.1 Campylobacter coli RM1875 plasmid pRM1875_3.4kbp, complete sequence',\n",
+ " 'NZ_CP007184.1 Campylobacter coli RM1875 plasmid pRM1875_35kb, complete sequence',\n",
+ " 'NZ_CP007181.1 Campylobacter coli RM4661, complete genome',\n",
+ " 'NZ_CP007182.1 Campylobacter coli RM4661 plasmid pRM4661_48kbp, complete sequence',\n",
+ " 'NZ_CP007179.1 Campylobacter coli RM5611, complete genome',\n",
+ " 'NZ_CP007180.1 Campylobacter coli RM5611 plasmid pRM5611_48kb, complete sequence',\n",
+ " 'NZ_CP004368.1 Burkholderia pseudomallei MSHR520 chromosome 1, complete sequence',\n",
+ " 'NZ_CP004369.1 Burkholderia pseudomallei MSHR520 chromosome 2, complete sequence',\n",
+ " 'NZ_CP004373.1 Gluconobacter oxydans DSM 3504, complete genome',\n",
+ " 'NZ_CP006571.1 Chlamydia avium 10DC88, complete genome',\n",
+ " 'NZ_CP006572.1 Chlamydia avium 10DC88 plasmid p10DC88, complete sequence',\n",
+ " 'NZ_CP007410.1 Pseudomonas brassicacearum strain DF41, complete genome',\n",
+ " 'NZ_CP007436.1 Bacillus pumilus strain MTCC B6033, complete genome',\n",
+ " 'NZ_CP007441.1 Pseudomonas stutzeri strain 28a24, complete genome',\n",
+ " 'NC_022904.2 Pandoraea pnomenusa 3kgm, complete genome',\n",
+ " 'NC_022198.1 Corynebacterium argentoratense DSM 44202, complete genome',\n",
+ " 'NC_022117.1 Chlamydia trachomatis strain F/1-93, complete genome',\n",
+ " 'NC_022118.1 Chlamydia trachomatis strain F/6-94, complete genome',\n",
+ " 'NC_022873.1 Bacillus thuringiensis YBT-1518, complete genome',\n",
+ " 'NC_020124.1 Bacillus thuringiensis YBT-1518 plasmid pBMB0228, complete sequence',\n",
+ " 'NC_022874.1 Bacillus thuringiensis YBT-1518 plasmid pBMB0229, complete sequence',\n",
+ " 'NC_022875.1 Bacillus thuringiensis YBT-1518 plasmid pBMB0230, complete sequence',\n",
+ " 'NC_022876.1 Bacillus thuringiensis YBT-1518 plasmid pBMB0231, complete sequence',\n",
+ " 'NC_022877.1 Bacillus thuringiensis YBT-1518 plasmid pBMB0232, complete sequence',\n",
+ " 'NC_022882.1 Bacillus thuringiensis YBT-1518 plasmid pBMB0233, complete sequence',\n",
+ " 'NC_022886.1 Helicobacter pylori BM012A, complete genome',\n",
+ " 'NC_022911.1 Helicobacter pylori BM012S, complete genome',\n",
+ " 'NZ_CP017152.1 Acinetobacter baumannii DU202, complete genome',\n",
+ " 'NZ_CP010979.1 Pseudomonas putida S13.1.2, complete genome',\n",
+ " 'NC_022900.1 Zymomonas mobilis subsp. mobilis str. CP4 = NRRL B-14023, complete genome',\n",
+ " 'NC_022901.1 Zymomonas mobilis subsp. mobilis str. CP4 = NRRL B-14023 plasmid, complete sequence',\n",
+ " 'NC_022913.1 Zymomonas mobilis subsp. mobilis str. CP4 = NRRL B-14023 plasmid, complete sequence',\n",
+ " 'NC_022902.1 Zymomonas mobilis subsp. mobilis str. CP4 = NRRL B-14023 plasmid, complete sequence',\n",
+ " 'NC_022903.1 Zymomonas mobilis subsp. mobilis str. CP4 = NRRL B-14023 plasmid, complete sequence',\n",
+ " 'NC_022910.1 Zymomonas mobilis subsp. mobilis str. CP4 = NRRL B-14023 plasmid, complete sequence',\n",
+ " 'NC_022909.1 Lactobacillus johnsonii N6.2, complete genome',\n",
+ " 'NZ_CP009365.1 Pseudomonas soli strain SJ10, complete genome',\n",
+ " 'NC_022964.1 Dehalococcoides mccartyi GY50, complete genome',\n",
+ " 'NZ_HG738867.1 Escherichia coli str. K-12 substr. MC4100 complete genome',\n",
+ " 'NC_022535.1 Rhizobium sp. IRBG74 circular chromosome, complete genome',\n",
+ " 'NC_022545.1 Rhizobium sp. IRBG74 linear chromosome, complete genome',\n",
+ " 'NC_022536.1 Rhizobium sp. IRBG74 plasmid IRBL74_p, complete sequence',\n",
+ " 'NZ_LN794217.1 Rickettsia monacensis, strain IrR/Munich, complete genome',\n",
+ " 'NZ_CP011913.1 Corynebacterium ulcerans FRC58, complete genome',\n",
+ " 'NC_019896.1 Bacillus subtilis subsp. subtilis str. BSP1, complete genome',\n",
+ " 'NC_019902.2 Thioalkalivibrio nitratireducens DSM 14787, complete genome',\n",
+ " 'NC_019908.1 Brachyspira pilosicoli P43/6/78, complete genome',\n",
+ " 'NC_019904.1 Echinicola vietnamensis DSM 17526, complete genome',\n",
+ " 'NC_019905.1 Pseudomonas putida HB3267, complete genome',\n",
+ " 'NC_019906.1 Pseudomonas putida HB3267 plasmid pPC9, complete sequence',\n",
+ " 'NC_019907.1 Liberibacter crescens BT-1, complete genome',\n",
+ " 'NC_019940.1 Thioflavicoccus mobilis 8321, complete genome',\n",
+ " 'NC_019941.1 Thioflavicoccus mobilis 8321 plasmid pTHIMO01, complete sequence',\n",
+ " 'NC_019936.1 Pseudomonas stutzeri RCH2, complete genome',\n",
+ " 'NC_019937.1 Pseudomonas stutzeri RCH2 plasmid pPSEST01, complete sequence',\n",
+ " 'NC_019938.1 Pseudomonas stutzeri RCH2 plasmid pPSEST02, complete sequence',\n",
+ " 'NC_019939.1 Pseudomonas stutzeri RCH2 plasmid pPSEST03, complete sequence',\n",
+ " 'NC_019955.1 Vibrio parahaemolyticus BB22OP chromosome 1, complete sequence',\n",
+ " 'NC_019971.1 Vibrio parahaemolyticus BB22OP chromosome 2, complete sequence',\n",
+ " 'NC_019970.1 Thermoanaerobacterium thermosaccharolyticum M0795, complete genome',\n",
+ " 'NC_019956.1 Thermoanaerobacterium thermosaccharolyticum M0795 plasmid pTHETHE01, complete sequence',\n",
+ " 'NC_019966.1 Mycobacterium sp. JS623, complete genome',\n",
+ " 'NC_019957.1 Mycobacterium sp. JS623 plasmid pMYCSM01, complete sequence',\n",
+ " 'NC_019958.1 Mycobacterium sp. JS623 plasmid pMYCSM02, complete sequence',\n",
+ " 'NC_019959.1 Mycobacterium sp. JS623 plasmid pMYCSM03, complete sequence',\n",
+ " 'NC_019978.1 Halobacteroides halobius DSM 5150, complete genome',\n",
+ " 'NC_019673.1 Saccharothrix espanaensis DSM 44229 complete genome',\n",
+ " 'NC_019949.1 Mycoplasma cynos C142 complete genome',\n",
+ " 'NC_019954.2 Tepidanaerobacter acetatoxydans Re1 complete genome',\n",
+ " 'NZ_CP007528.1 Salmonella enterica subsp. enterica serovar Enteritidis str. CDC_2010K_0968, complete genome',\n",
+ " 'NZ_CP007529.1 Salmonella enterica subsp. enterica serovar Enteritidis str. CDC_2010K_0968 plasmid00, complete sequence',\n",
+ " 'NZ_CP012347.1 Salmonella enterica subsp. enterica serovar Pullorum str. ATCC 9120, complete genome',\n",
+ " 'NZ_CP012348.1 Salmonella enterica subsp. enterica serovar Pullorum str. ATCC 9120 plasmid pCFSAN000725_01, complete sequence',\n",
+ " 'NZ_CP007255.1 Rhodococcus erythropolis R138, complete genome',\n",
+ " 'NZ_CP007256.1 Rhodococcus erythropolis R138 plasmid pCRE138, complete sequence',\n",
+ " 'NZ_CP007257.1 Rhodococcus erythropolis R138 plasmid pLRE138, complete sequence',\n",
+ " 'NZ_CP015880.1 Ensifer adhaerens strain Casida A chromosome, complete genome',\n",
+ " 'NZ_CP015881.1 Ensifer adhaerens strain Casida A plasmid pCasidaAA, complete sequence',\n",
+ " 'NZ_CP015882.1 Ensifer adhaerens strain Casida A plasmid pCasidaAB, complete sequence',\n",
+ " 'NZ_CP007691.1 Brucella suis bv. 2 strain PT09143 chromosome I, complete sequence',\n",
+ " 'NZ_CP007692.1 Brucella suis bv. 2 strain PT09143 chromosome II, complete sequence',\n",
+ " 'NZ_CP007693.1 Brucella suis bv. 2 strain PT09172 chromosome I, complete sequence',\n",
+ " 'NZ_CP007694.1 Brucella suis bv. 2 strain PT09172 chromosome II, complete sequence',\n",
+ " 'NZ_CP007697.1 Brucella suis bv. 2 strain Bs364CITA chromosome I, complete sequence',\n",
+ " 'NZ_CP007698.1 Brucella suis bv. 2 strain Bs364CITA chromosome II, complete sequence',\n",
+ " 'NZ_CP007720.1 Brucella suis bv. 2 strain Bs396CITA chromosome I, complete sequence',\n",
+ " 'NZ_CP007721.1 Brucella suis bv. 2 strain Bs396CITA chromosome II, complete sequence',\n",
+ " 'NZ_CP007805.1 Haemophilus influenzae CGSHiCZ412602, complete genome',\n",
+ " 'NZ_CP007803.1 Mycobacterium tuberculosis K, complete genome',\n",
+ " 'NZ_CP006696.1 Xylella fastidiosa subsp. sandyi Ann-1, complete genome',\n",
+ " 'NZ_CP006697.1 Xylella fastidiosa subsp. sandyi Ann-1 plasmid unnamed1, complete sequence',\n",
+ " 'NZ_CP006740.1 Xylella fastidiosa MUL0034, complete genome',\n",
+ " 'NZ_CP006739.1 Xylella fastidiosa MUL0034 plasmid unnamed2, complete sequence',\n",
+ " 'NZ_CP006986.1 Rhizobium sp. IE4771 chromosome, complete genome',\n",
+ " 'NZ_CP006987.1 Rhizobium sp. IE4771 plasmid pRetIE4771a, complete sequence',\n",
+ " 'NZ_CP006988.1 Rhizobium sp. IE4771 plasmid pRetIE4771b, complete sequence',\n",
+ " 'NZ_CP006989.1 Rhizobium sp. IE4771 plasmid pRetIE4771c, complete sequence',\n",
+ " 'NZ_CP006990.1 Rhizobium sp. IE4771 plasmid pRetIE4771d, complete sequence',\n",
+ " 'NZ_CP006991.1 Rhizobium sp. IE4771 plasmid pRetIE4771e, complete sequence',\n",
+ " 'NZ_CP008696.1 Pseudomonas chlororaphis strain PA23, complete genome',\n",
+ " 'NZ_CP006819.1 Streptococcus thermophilus ASCC 1275, complete genome',\n",
+ " 'NZ_CP007695.1 Brucella suis bv. 2 strain Bs143CITA chromosome I, complete sequence',\n",
+ " 'NZ_CP007696.1 Brucella suis bv. 2 strain Bs143CITA chromosome II, complete sequence',\n",
+ " 'NC_020533.1 Staphylococcus aureus subsp. aureus ST228 complete genome, isolate 16035',\n",
+ " 'NC_020534.1 Staphylococcus aureus subsp. aureus ST228 plasmid pI4T8 complete sequence, isolate 16035',\n",
+ " 'NC_020566.1 Staphylococcus aureus subsp. aureus ST228 complete genome, isolate 16125',\n",
+ " 'NC_020535.1 Staphylococcus aureus subsp. aureus ST228 plasmid pI5S5 complete sequence, isolate 16125',\n",
+ " 'NC_020568.1 Staphylococcus aureus subsp. aureus ST228 complete genome, isolate 18583',\n",
+ " 'NC_020539.1 Staphylococcus aureus subsp. aureus ST228 plasmid pI8T7 complete sequence, isolate 18583',\n",
+ " 'NC_021173.1 Burkholderia thailandensis MSMB121 chromosome 1, complete sequence',\n",
+ " 'NC_021174.1 Burkholderia thailandensis MSMB121 chromosome 2, complete sequence',\n",
+ " 'NC_021176.1 Salmonella enterica subsp. enterica serovar Typhi str. Ty21a, complete genome',\n",
+ " 'NC_021175.1 Streptococcus cristatus AS 1.3089, complete genome',\n",
+ " 'NC_021177.1 Streptomyces fulvissimus DSM 40593, complete sequence',\n",
+ " 'NZ_CP010539.1 Mycoplasma pneumoniae 19294, complete genome',\n",
+ " 'NC_021182.1 Clostridium pasteurianum BC1, complete genome',\n",
+ " 'NC_021183.1 Clostridium pasteurianum BC1 plasmid pCLOPA01, complete sequence',\n",
+ " 'NC_021181.2 Lactobacillus acidophilus La-14, complete genome',\n",
+ " 'NC_021194.1 Mycobacterium tuberculosis EAI5/NITR206, complete genome',\n",
+ " 'NC_021191.1 Actinoplanes sp. N902-109, complete genome',\n",
+ " 'NC_021200.1 Mycobacterium avium subsp. paratuberculosis MAP4, complete genome',\n",
+ " 'NC_021213.1 Streptococcus suis TL13, complete genome',\n",
+ " 'NZ_CP009144.1 Sinorhizobium meliloti strain RMO17, complete genome',\n",
+ " 'NZ_CP009145.1 Sinorhizobium meliloti strain RMO17 plasmid pSymA, complete sequence',\n",
+ " 'NZ_CP009146.1 Sinorhizobium meliloti strain RMO17 plasmid pSymB, complete sequence',\n",
+ " 'NZ_CP009215.1 Corynebacterium ureicelerivorans strain IMMIB RIV-2301, complete genome',\n",
+ " 'NZ_CP009216.1 Corynebacterium ureicelerivorans strain IMMIB RIV-2301 plasmid unnamed, complete sequence',\n",
+ " 'NZ_CP008853.1 Bacillus anthracis strain Cvac02, complete genome',\n",
+ " 'NZ_CP008855.1 Bacillus sp. X1(2014), complete genome',\n",
+ " 'NZ_CP009278.1 Sphingobacterium sp. ML3W, complete genome',\n",
+ " 'NZ_CP007607.1 Bacillus thuringiensis serovar kurstaki str. YBT-1520, complete genome',\n",
+ " 'NZ_CP007612.1 Bacillus thuringiensis serovar kurstaki str. YBT-1520 plasmid pBMB11, complete sequence',\n",
+ " 'NZ_CP007608.1 Bacillus thuringiensis serovar kurstaki str. YBT-1520 plasmid pBMB2062, complete sequence',\n",
+ " 'NZ_CP007615.1 Bacillus thuringiensis serovar kurstaki str. YBT-1520 plasmid pBMB293, complete sequence',\n",
+ " 'NZ_CP007616.1 Bacillus thuringiensis serovar kurstaki str. YBT-1520 plasmid pBMB400, complete sequence',\n",
+ " 'NZ_CP007613.1 Bacillus thuringiensis serovar kurstaki str. YBT-1520 plasmid pBMB69, complete sequence',\n",
+ " 'NZ_CP007609.1 Bacillus thuringiensis serovar kurstaki str. YBT-1520 plasmid pBMB7921, complete sequence',\n",
+ " 'NZ_CP007610.1 Bacillus thuringiensis serovar kurstaki str. YBT-1520 plasmid pBMB8240, complete sequence',\n",
+ " 'NZ_CP007611.1 Bacillus thuringiensis serovar kurstaki str. YBT-1520 plasmid pBMB8513, complete sequence',\n",
+ " 'NZ_CP007614.1 Bacillus thuringiensis serovar kurstaki str. YBT-1520 plasmid pBMB95, complete sequence',\n",
+ " 'NZ_CP003424.1 Serratia sp. SCBI, complete genome',\n",
+ " 'NZ_CP003425.1 Serratia sp. SCBI plasmid SCBI_Pl, complete sequence',\n",
+ " 'NZ_CP006683.1 Melissococcus plutonius S1, complete genome',\n",
+ " 'NZ_CP006684.1 Melissococcus plutonius S1 plasmid pMEPL_178, complete sequence',\n",
+ " 'NZ_CP009239.1 Cellulophaga lytica strain HI1, complete genome',\n",
+ " 'NZ_CP009089.1 Salmonella enterica subsp. enterica serovar Enteritidis strain OLF-SE7-100819, complete genome',\n",
+ " 'NZ_CP008897.1 Enterobacter cloacae ECNIH3, complete genome',\n",
+ " 'NZ_CP008898.1 Enterobacter cloacae ECNIH3 plasmid pENT-576, complete sequence',\n",
+ " 'NZ_CP008899.1 Enterobacter cloacae ECNIH3 plasmid pENT-8a4, complete sequence',\n",
+ " 'NZ_CP008900.1 Enterobacter cloacae ECNIH3 plasmid pENT-d4a, complete sequence',\n",
+ " 'NZ_CP008901.1 Enterobacter cloacae ECNIH3 plasmid pKPC-47e, complete sequence',\n",
+ " 'NZ_CP009090.1 Salmonella enterica subsp. enterica serovar Enteritidis strain OLF-SE8-1021710, complete genome',\n",
+ " 'NZ_CP008905.1 Enterobacter cloacae ECR091, complete genome',\n",
+ " 'NZ_CP008906.1 Enterobacter cloacae ECR091 plasmid pENT-08e, complete sequence',\n",
+ " 'NZ_CP008907.1 Enterobacter cloacae ECR091 plasmid pENT-4bd, complete sequence',\n",
+ " 'NZ_CP008908.1 Enterobacter cloacae ECR091 plasmid pKPC-47e, complete sequence',\n",
+ " 'NZ_CP009091.1 Salmonella enterica subsp. enterica serovar Enteritidis strain OLF-SE9-10012, complete genome',\n",
+ " 'NZ_CP008943.1 Yersinia pseudotuberculosis strain ATCC 6904, complete genome',\n",
+ " 'NZ_CP009092.1 Salmonella enterica subsp. enterica serovar Enteritidis strain OLF-SE10-10052, complete genome',\n",
+ " 'NZ_CP009093.1 Salmonella enterica subsp. enterica serovar Enteritidis strain OLF-SE11-10058, complete genome',\n",
+ " 'NZ_CP009085.2 Salmonella enterica subsp. enterica serovar Enteritidis strain OLF-SE3-98983-4, complete genome',\n",
+ " 'NZ_CP009084.2 Salmonella enterica subsp. enterica serovar Enteritidis strain OLF-SE2-98984-6, complete genome',\n",
+ " 'NZ_CP007229.1 Mycoplasma dispar strain ATCC 27140, complete genome',\n",
+ " 'NZ_CP016174.1 Amycolatopsis orientalis strain B-37, complete genome',\n",
+ " 'NZ_CP010954.1 Sphingobium sp. YBL2, complete genome',\n",
+ " 'NZ_CP010955.1 Sphingobium sp. YBL2 plasmid 1pYBL2-1, complete sequence',\n",
+ " 'NZ_CP010956.1 Sphingobium sp. YBL2 plasmid 2pYBL2-2, complete sequence',\n",
+ " 'NZ_CP010957.1 Sphingobium sp. YBL2 plasmid 3pYBL2-3, complete sequence',\n",
+ " 'NZ_CP010958.1 Sphingobium sp. YBL2 plasmid 4pYBL2-4, complete sequence',\n",
+ " 'NZ_CP010959.1 Sphingobium sp. YBL2 plasmid 5pYBL2-5, complete sequence',\n",
+ " 'NZ_CP010960.1 Sphingobium sp. YBL2 plasmid 6pYBL2-6, complete sequence',\n",
+ " 'NZ_CP009677.1 Mycoplasma hominis strain AF1, complete genome',\n",
+ " 'NZ_CP007166.1 Xanthomonas oryzae pv. oryzae PXO86, complete genome',\n",
+ " 'NZ_CP010976.1 Paenibacillus sp. IHBB 10380, complete genome',\n",
+ " 'NZ_CP010977.1 Paenibacillus sp. IHBB 10380 plasmid, complete sequence',\n",
+ " 'NZ_CP011005.1 Arthrobacter sp. IHBB 11108, complete genome',\n",
+ " 'NZ_CP011006.1 Arthrobacter sp. IHBB 11108 plasmid pAG001, complete sequence',\n",
+ " 'NZ_CP011004.1 Listeria monocytogenes strain N2306, complete genome',\n",
+ " 'NZ_CP007699.2 Streptomyces lydicus strain A02 chromosome, complete genome',\n",
+ " 'NZ_LN680001.1 Bacillus sp. BS34A genome assembly, chromosome: I',\n",
+ " 'NZ_LM995445.1 Mycoplasma capricolum subsp. capripneumoniae genome assembly 9231-Abomsa assembly V8, chromosome : I',\n",
+ " 'NZ_LN554882.1 Chlamydophila abortus genome assembly CAAB7, chromosome : 1',\n",
+ " 'NZ_LM995446.1 Escherichia coli genome assembly EcRV308Chr, chromosome : 1',\n",
+ " 'NZ_LM997412.1 Peptoniphilus sp. ING2-D1G genome assembly, chromosome: I',\n",
+ " 'NZ_LN794158.1 Candidatus Methylopumilus turicensis genome assembly Candidatus Methylopumilus turicensis MMS-10A-171, chromosome : 1',\n",
+ " 'NZ_LM651928.1 Shigella flexneri genome assembly NCTC1, chromosome : 1',\n",
+ " 'NZ_LK936442.1 Burkholderia pseudomallei genome assembly BP_3921g, chromosome : 1',\n",
+ " 'NZ_LK936443.1 Burkholderia pseudomallei genome assembly BP_3921g, chromosome : 2',\n",
+ " 'NZ_LN614827.1 Legionella fallonii LLAP-10 genome assembly LFA, chromosome : I',\n",
+ " 'NZ_LN614828.1 Legionella fallonii LLAP-10 genome assembly LFA, plasmid : II',\n",
+ " 'NZ_LN614829.1 Legionella fallonii LLAP-10 genome assembly LFA, plasmid : III',\n",
+ " 'NZ_CP007686.1 Listeria monocytogenes strain L2624, complete genome',\n",
+ " 'NZ_CP007685.1 Listeria monocytogenes strain L2676, complete genome',\n",
+ " 'NZ_CP011511.1 Shigella boydii strain ATCC 9210, complete genome',\n",
+ " 'NZ_CP007684.1 Listeria monocytogenes strain L2626, complete genome',\n",
+ " 'NZ_CP011501.1 Pandoraea apista strain AU2161, complete genome',\n",
+ " 'NZ_CP011509.1 Archangium gephyra strain DSM 2261, complete genome',\n",
+ " 'NZ_CP009498.1 Endomicrobium proavitum strain Rsa215, complete genome',\n",
+ " 'NZ_CP011827.2 Xanthomonas citri pv. citri strain jx-6, complete genome',\n",
+ " 'NZ_CP013665.1 Xanthomonas citri pv. citri strain jx-6 plasmid pXAC33, complete sequence',\n",
+ " 'NZ_CP013664.1 Xanthomonas citri pv. citri strain jx-6 plasmid pXAC64, complete sequence',\n",
+ " 'NZ_CP011805.1 Altererythrobacter marensis strain KCTC 22370, complete genome',\n",
+ " 'NZ_CP007601.1 Staphylococcus capitis subsp. capitis strain AYP1020, complete genome',\n",
+ " 'NZ_CP007602.1 Staphylococcus capitis subsp. capitis strain AYP1020 plasmid pAYP1020, complete sequence',\n",
+ " 'NZ_CP011503.1 Burkholderia pyrrocinia strain DSM 10685 chromosome 1, complete sequence',\n",
+ " 'NZ_CP011504.1 Burkholderia pyrrocinia strain DSM 10685 chromosome 2, complete sequence',\n",
+ " 'NZ_CP011505.1 Burkholderia pyrrocinia strain DSM 10685 chromosome 3, complete sequence',\n",
+ " 'NZ_CP011506.1 Burkholderia pyrrocinia strain DSM 10685 plasmid p2327, complete sequence',\n",
+ " 'NZ_CP011770.1 Croceicoccus naphthovorans strain PQ-2, complete genome',\n",
+ " 'NZ_CP011771.1 Croceicoccus naphthovorans strain PQ-2 plasmid p1, complete sequence',\n",
+ " 'NZ_CP011772.1 Croceicoccus naphthovorans strain PQ-2 plasmid p2, complete sequence',\n",
+ " 'NZ_CP011807.3 Pandoraea faecigallinarum strain DSM 23572, complete genome',\n",
+ " 'NZ_CP011808.2 Pandoraea faecigallinarum strain DSM 23572 plasmid pPF72-1, complete sequence',\n",
+ " 'NZ_CP011809.2 Pandoraea faecigallinarum strain DSM 23572 plasmid pPF72-2, complete sequence',\n",
+ " 'NZ_CP006636.1 Escherichia coli PCN061, complete genome',\n",
+ " 'NZ_CP006637.1 Escherichia coli PCN061 plasmid PCN061p1, complete sequence',\n",
+ " 'NZ_CP006638.1 Escherichia coli PCN061 plasmid PCN061p2, complete sequence',\n",
+ " 'NZ_CP006639.1 Escherichia coli PCN061 plasmid PCN061p3, complete sequence',\n",
+ " 'NZ_CP006640.1 Escherichia coli PCN061 plasmid PCN061p4, complete sequence',\n",
+ " 'NZ_CP006641.1 Escherichia coli PCN061 plasmid PCN061p5, complete sequence',\n",
+ " 'NZ_CP006642.1 Escherichia coli PCN061 plasmid PCN061p6, complete sequence',\n",
+ " 'NZ_CP009743.1 Burkholderia contaminans strain MS14 chromosome 1, complete sequence',\n",
+ " 'NZ_CP009744.1 Burkholderia contaminans strain MS14 chromosome 2, complete sequence',\n",
+ " 'NZ_CP009745.1 Burkholderia contaminans strain MS14 chromosome 3, complete sequence',\n",
+ " 'NZ_CP011855.1 Spiroplasma atrichopogonis strain GNAT3597, complete genome',\n",
+ " 'NZ_CP011856.1 Spiroplasma eriocheiris strain DSM 21848, complete genome',\n",
+ " 'NZ_CP011798.1 Enterobacter cloacae strain UW5, complete genome',\n",
+ " 'NZ_CP007667.1 Neisseria meningitidis strain B6116/77, complete genome',\n",
+ " 'NZ_CP007668.1 Neisseria meningitidis M0579, complete genome',\n",
+ " 'NZ_CP011882.1 Bacillus subtilis strain TO-A JPC, complete genome',\n",
+ " 'NZ_CP011804.1 Clostridium carboxidivorans P7 plasmid, complete sequence',\n",
+ " 'NZ_CP011803.1 Clostridium carboxidivorans P7, complete genome',\n",
+ " 'NZ_CP005969.1 Pseudomonas syringae pv. syringae B301D, complete genome',\n",
+ " 'NZ_CP007584.2 Salmonella enterica subsp. enterica serovar Anatum str. USDA-ARS-USMARC-1735, complete genome',\n",
+ " 'NZ_CP014707.1 Salmonella enterica subsp. enterica serovar Anatum strain USMARC-1735 plasmid pSAN1-1735, complete sequence',\n",
+ " 'NZ_CP006003.1 Myxococcus fulvus 124B02, complete genome',\n",
+ " 'NZ_CP011374.1 Moraxella bovoculi strain 58069, complete genome',\n",
+ " 'NZ_CP011375.1 Moraxella bovoculi strain 58069 plasmid, complete sequence',\n",
+ " 'NZ_CP011376.1 Moraxella bovoculi strain 22581, complete genome',\n",
+ " 'NZ_CP011377.1 Moraxella bovoculi strain 23343, complete genome',\n",
+ " 'NZ_CP011378.1 Moraxella bovoculi strain 28389, complete genome',\n",
+ " 'NZ_CP011379.1 Moraxella bovoculi strain 33362, complete genome',\n",
+ " 'NZ_CP011380.2 Moraxella bovoculi strain 57922, complete genome',\n",
+ " 'NZ_CP011365.1 Salmonella enterica subsp. enterica serovar Typhimurium strain FORC_015, complete genome',\n",
+ " 'NZ_CP007497.1 Streptococcus suis strain ZY05719, complete genome',\n",
+ " 'NZ_CP007537.1 Streptococcus pyogenes strain AP1, complete genome',\n",
+ " 'NZ_CP009922.2 Streptomyces xiamenensis strain 318, complete genome',\n",
+ " 'NZ_CP011114.1 Paenibacillus durus ATCC 35681, complete genome',\n",
+ " 'NZ_CP011366.1 Salinicoccus halodurans strain H3B36, complete genome',\n",
+ " 'NZ_CP011398.2 Listeria monocytogenes strain CFSAN008100 chromosome, complete genome',\n",
+ " 'NZ_CP011399.1 Listeria monocytogenes strain CFSAN008100 plasmid pCFSAN008100, complete sequence',\n",
+ " 'NZ_AP012555.1 Mycobacterium avium subsp. hominissuis TH135 chromosomal DNA, complete genome',\n",
+ " 'NZ_AP012556.1 Mycobacterium avium subsp. hominissuis TH135 plasmid pMAH135 DNA, complete genome',\n",
+ " 'NZ_AP013354.1 Helicobacter pylori 26695-1 DNA, complete genome',\n",
+ " 'NZ_AP013356.1 Helicobacter pylori 26695-1CL DNA, complete genome',\n",
+ " 'NZ_AP013355.1 Helicobacter pylori 26695-1CH DNA, complete genome',\n",
+ " 'NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome',\n",
+ " 'NZ_AP014582.1 Bordetella bronchiseptica DNA, complete genome, strain: S798',\n",
+ " 'NZ_AP013294.1 Bacillus sp. OxB-1 DNA, complete genome',\n",
+ " 'NZ_AP014524.1 Vibrio cholerae MS6 DNA, complete genome, chromosome 1',\n",
+ " 'NZ_AP014525.1 Vibrio cholerae MS6 DNA, complete genome, chromosome 2',\n",
+ " 'NZ_AP012549.1 Cyanobacterium endosymbiont of Epithemia turgida isolate EtSB Lake Yunoko DNA, complete genome',\n",
+ " 'NZ_AP014646.1 Pseudomonas aeruginosa DNA, complete genome, strain: NCGM 1984',\n",
+ " 'NZ_AP014622.1 Pseudomonas aeruginosa DNA, complete genome, strain: NCGM 1900',\n",
+ " 'NZ_AP014658.1 Bifidobacterium longum DNA, complete genome, strain: 105-A',\n",
+ " 'NZ_AP013028.1 Wolbachia endosymbiont of Cimex lectularius DNA, complete genome',\n",
+ " 'NZ_CP026055.1 Aeromonas caviae strain FDAARGOS_72 chromosome, complete genome',\n",
+ " 'NZ_CP026052.1 Salmonella enterica strain FDAARGOS_70 chromosome, complete genome',\n",
+ " 'NZ_CP026053.1 Salmonella enterica strain FDAARGOS_70 plasmid unnamed1, complete sequence',\n",
+ " 'NZ_CP026054.1 Salmonella enterica strain FDAARGOS_70 plasmid unnamed2, complete sequence',\n",
+ " 'NZ_CP026051.1 Proteus mirabilis strain FDAARGOS_67 chromosome, complete genome',\n",
+ " 'NZ_CP026050.1 Serratia marcescens strain FDAARGOS_65 chromosome, complete genome',\n",
+ " 'NZ_CP026047.1 Raoultella planticola strain FDAARGOS_64 chromosome, complete genome',\n",
+ " 'NZ_CP026048.1 Raoultella planticola strain FDAARGOS_64 plasmid unnamed1, complete sequence',\n",
+ " 'NZ_CP026049.1 Raoultella planticola strain FDAARGOS_64 plasmid unnamed2, complete sequence',\n",
+ " 'NZ_CP026046.1 Morganella morganii strain FDAARGOS_63 chromosome, complete genome',\n",
+ " 'NZ_CP026045.1 Citrobacter freundii strain FDAARGOS_61 chromosome, complete genome',\n",
+ " 'NZ_CP026044.1 Proteus mirabilis strain FDAARGOS_60 chromosome, complete genome',\n",
+ " 'NZ_CP009850.1 Enterobacter cloacae strain ECNIH4, complete genome',\n",
+ " 'NZ_CP009851.1 Enterobacter cloacae strain ECNIH4 plasmid pENT-c88, complete sequence',\n",
+ " 'NZ_CP009852.1 Enterobacter cloacae strain ECNIH4 plasmid pENT-e56, complete sequence',\n",
+ " 'NZ_CP009853.1 Enterobacter cloacae strain ECNIH4 plasmid pKPC-860, complete sequence',\n",
+ " 'NZ_CP009880.1 Pantoea sp. PSNIH1, complete genome',\n",
+ " 'NZ_CP009881.1 Pantoea sp. PSNIH1 plasmid pKPC-1c5, complete sequence',\n",
+ " 'NZ_CP010325.1 Pantoea sp. PSNIH1 plasmid pPSP-057, complete sequence',\n",
+ " 'NZ_CP009882.1 Pantoea sp. PSNIH1 plasmid pPSP-26e, complete sequence',\n",
+ " 'NZ_CP010326.1 Pantoea sp. PSNIH1 plasmid pPSP-3a9, complete sequence',\n",
+ " 'NZ_CP009883.1 Pantoea sp. PSNIH1 plasmid pPSP-a3e, complete sequence',\n",
+ " 'NZ_CP009884.1 Pantoea sp. PSNIH1 plasmid pPSP-ee2, complete sequence',\n",
+ " 'NZ_CP009854.1 Enterobacter cloacae strain ECNIH5, complete genome',\n",
+ " 'NZ_CP009855.1 Enterobacter cloacae strain ECNIH5 plasmid pENT-22e, complete sequence',\n",
+ " 'NZ_CP009856.1 Enterobacter cloacae strain ECNIH5 plasmid pENT-784, complete sequence',\n",
+ " 'NZ_CP009857.1 Enterobacter cloacae strain ECNIH5 plasmid pENT-d0d, complete sequence',\n",
+ " 'NZ_CP009858.1 Enterobacter cloacae strain ECNIH5 plasmid pKPC-47e, complete sequence',\n",
+ " 'NZ_CP009859.1 Escherichia coli strain ECONIH1, complete genome',\n",
+ " 'NZ_CP009860.1 Escherichia coli strain ECONIH1 plasmid pECO-824, complete sequence',\n",
+ " 'NZ_CP009861.1 Escherichia coli strain ECONIH1 plasmid pECO-b75, complete sequence',\n",
+ " 'NZ_CP009862.1 Escherichia coli strain ECONIH1 plasmid pKPC-629, complete sequence',\n",
+ " 'NZ_CP009863.1 Klebsiella pneumoniae subsp. pneumoniae strain KPNIH29, complete genome',\n",
+ " 'NZ_CP009864.1 Klebsiella pneumoniae subsp. pneumoniae strain KPNIH29 plasmid pKPC-e4e, complete sequence',\n",
+ " 'NZ_CP009865.1 Klebsiella pneumoniae subsp. pneumoniae strain KPNIH29 plasmid pKPN-80a, complete sequence',\n",
+ " 'NZ_CP009866.1 Pantoea sp. PSNIH2, complete genome',\n",
+ " 'NZ_CP009867.1 Pantoea sp. PSNIH2 plasmid pKPC-56a, complete sequence',\n",
+ " 'NZ_CP009868.1 Pantoea sp. PSNIH2 plasmid pPSP-100, complete sequence',\n",
+ " 'NZ_CP009869.1 Pantoea sp. PSNIH2 plasmid pPSP-75c, complete sequence',\n",
+ " 'NZ_CP009870.1 Pantoea sp. PSNIH2 plasmid pPSP-b98, complete sequence',\n",
+ " 'NZ_CP009871.1 Pantoea sp. PSNIH2 plasmid pPSP-cd6, complete sequence',\n",
+ " 'NZ_CP012074.1 Prevotella fusca JCM 17724 strain W1435 chromosome 1, complete sequence',\n",
+ " 'NZ_CP012075.1 Prevotella fusca JCM 17724 strain W1435 chromosome 2, complete sequence',\n",
+ " 'NZ_CP012067.1 Aggregatibacter aphrophilus strain W10433, complete genome',\n",
+ " 'NZ_CP012072.1 Actinomyces meyeri strain W712, complete genome',\n",
+ " 'NZ_CP012073.1 Ottowia sp. oral taxon 894 strain W10237, complete genome',\n",
+ " 'NZ_CP012037.1 Francisella tularensis subsp. tularensis strain WY96, complete genome',\n",
+ " 'NZ_CP012328.1 Spiroplasma turonicum strain Tab4c, complete genome',\n",
+ " 'NZ_CP012332.1 Vulgatibacter incomptus strain DSM 27710, complete genome',\n",
+ " 'NZ_CP011786.1 Bifidobacterium actinocoloniiforme DSM 22766, complete genome',\n",
+ " 'NZ_CP011995.1 Porphyromonas gingivalis strain A7436, complete genome',\n",
+ " 'NZ_CP011339.1 Microcystis panniformis FACHB-1757, complete genome',\n",
+ " 'NZ_CP010319.1 Streptococcus agalactiae strain GBS85147, complete genome',\n",
+ " 'NZ_CP012299.1 Microbacterium sp. CGR1, complete genome',\n",
+ " 'NZ_CP011929.1 Marinobacter sp. CP1, complete genome',\n",
+ " 'NZ_CP012357.1 Spiroplasma litorale strain TN-1, complete genome',\n",
+ " 'NZ_CP012358.1 Oblitimonas alkaliphila strain B4199 chromosome, complete genome',\n",
+ " 'NZ_CP012359.1 Oblitimonas alkaliphila strain C6819 chromosome, complete genome',\n",
+ " 'NZ_CP012360.1 Oblitimonas alkaliphila strain C6918 chromosome, complete genome',\n",
+ " 'NZ_CP012362.1 Oblitimonas alkaliphila strain D3318 chromosome, complete genome',\n",
+ " 'NZ_CP012363.1 Oblitimonas alkaliphila strain E1086 chromosome, complete genome',\n",
+ " 'NZ_CP014773.1 Mucilaginibacter sp. PAMC 26640 chromosome, complete genome',\n",
+ " 'NZ_CP014772.1 Mucilaginibacter sp. PAMC 26640 plasmid unnamed, complete sequence',\n",
+ " 'NZ_CP014771.1 Hymenobacter sp. PAMC 26554 chromosome, complete genome',\n",
+ " 'NZ_CP014769.1 Hymenobacter sp. PAMC 26554 plasmid unnamed1, complete sequence',\n",
+ " 'NZ_CP014770.1 Hymenobacter sp. PAMC 26554 plasmid unnamed2, complete sequence',\n",
+ " 'NZ_CP014805.2 Elizabethkingia anophelis strain CSID_3015183678 chromosome, complete genome',\n",
+ " 'NZ_CP014858.1 Bacillus subtilis subsp. subtilis strain D12-5 chromosome, complete genome',\n",
+ " 'NZ_CP014783.1 Bacillus amyloliquefaciens strain B15 chromosome, complete genome',\n",
+ " 'NZ_CP014790.1 Listeria monocytogenes strain 2015TE24968 chromosome, complete genome',\n",
+ " 'NZ_CP015985.1 Listeria monocytogenes strain 2015TE24968 plasmid pl2015TE24968, complete sequence',\n",
+ " 'NZ_CP014840.1 Bacillus subtilis subsp. globigii strain ATCC 49760 chromosome, complete genome',\n",
+ " 'NZ_CP014784.1 Pseudomonas alcaligenes strain NEB 585, complete genome',\n",
+ " 'NZ_CP014835.1 Streptococcus halotolerans strain HTS9 chromosome, complete genome',\n",
+ " 'NZ_CP014856.1 Lysinibacillus sphaericus III(3)7, complete genome',\n",
+ " 'NZ_CP014857.1 Lysinibacillus sphaericus III(3)7 plasmid, complete sequence',\n",
+ " 'NZ_CP014847.1 Bacillus thuringiensis strain HD12, complete sequence',\n",
+ " 'NZ_CP014848.1 Bacillus thuringiensis strain HD12 plasmid pHD120017, complete sequence',\n",
+ " 'NZ_CP014849.1 Bacillus thuringiensis strain HD12 plasmid pHD120038, complete sequence',\n",
+ " 'NZ_CP014850.1 Bacillus thuringiensis strain HD12 plasmid pHD120039, complete sequence',\n",
+ " 'NZ_CP014851.1 Bacillus thuringiensis strain HD12 plasmid pHD120112, complete sequence',\n",
+ " 'NZ_CP014852.1 Bacillus thuringiensis strain HD12 plasmid pHD120161, complete sequence',\n",
+ " 'NZ_CP014853.1 Bacillus thuringiensis strain HD12 plasmid pHD120345, complete sequence',\n",
+ " 'NZ_CP014949.1 Enterococcus faecalis strain LD33, complete genome',\n",
+ " 'NZ_CP014991.1 Helicobacter himalayensis strain YS1, complete genome',\n",
+ " 'NZ_CP014352.1 Acidipropionibacterium acidipropionici strain ATCC 55737 chromosome, complete genome',\n",
+ " 'NZ_CP014353.1 Acidipropionibacterium acidipropionici strain ATCC 55737 plasmid unnamed, complete sequence',\n",
+ " 'NZ_CP014867.1 Pseudomonas chlororaphis isolate 189 chromosome, complete genome',\n",
+ " 'NZ_CP014861.1 Erysipelothrix rhusiopathiae strain GXBY-1 chromosome, complete genome',\n",
+ " 'NZ_CP014865.1 Rickettsia prowazekii strain Naples-1 chromosome, complete genome',\n",
+ " 'NZ_CP015004.1 Bacillus subtilis strain SZMC 6179J, complete genome',\n",
+ " 'NZ_CP015005.1 Aminobacter aminovorans strain KCTC 2477, complete genome',\n",
+ " 'NZ_CP015006.1 Aminobacter aminovorans strain KCTC 2477 plasmid pAA01, complete sequence',\n",
+ " 'NZ_CP015007.1 Aminobacter aminovorans strain KCTC 2477 plasmid pAA02, complete sequence',\n",
+ " 'NZ_CP015008.1 Aminobacter aminovorans strain KCTC 2477 plasmid pAA03, complete sequence',\n",
+ " 'NZ_CP015009.1 Aminobacter aminovorans strain KCTC 2477 plasmid pAA04, complete sequence',\n",
+ " 'NZ_CP010838.1 Bordetella pertussis strain H374, complete genome',\n",
+ " 'NZ_CP010839.1 Bordetella pertussis strain H378, complete genome',\n",
+ " 'NZ_CP010840.1 Bordetella pertussis strain H379, complete genome',\n",
+ " 'NZ_CP014029.2 Klebsiella aerogenes strain FDAARGOS_152 chromosome, complete genome',\n",
+ " 'NZ_CP014030.2 Citrobacter sp. FDAARGOS_156 strain FDAARGOS_155 chromosome, complete genome',\n",
+ " 'NZ_CP014031.2 Hafnia paralvei strain FDAARGOS_158 chromosome, complete genome',\n",
+ " 'NZ_CP014268.2 Escherichia coli B strain C2566, complete genome',\n",
+ " 'NZ_CP014269.1 Escherichia coli B strain C3029, complete genome',\n",
+ " 'NZ_CP014270.1 Escherichia coli K-12 strain DHB4, complete genome',\n",
+ " 'NZ_CP014271.1 Escherichia coli K-12 strain DHB4 plasmid F128-(DHB4), complete sequence',\n",
+ " 'NZ_CP014272.1 Escherichia coli K-12 strain C3026, complete genome',\n",
+ " 'NZ_CP014273.1 Escherichia coli K-12 strain C3026 plasmid F128-(C3026), complete sequence',\n",
+ " 'NZ_CP014326.1 Streptococcus mitis strain SVGS_061, complete genome',\n",
+ " 'NZ_CP014223.1 [Clostridium] propionicum DSM 1682, complete genome',\n",
+ " 'NZ_CP014279.1 Corynebacterium stationis strain ATCC 6872, complete genome',\n",
+ " 'NZ_CP013926.1 Alteromonas stellipolaris strain LMG 21861, complete genome',\n",
+ " 'NZ_CP013927.1 Alteromonas stellipolaris strain LMG 21861 plasmid pASTE61-200, complete sequence',\n",
+ " 'NZ_CP013932.1 Alteromonas sp. Mac1, complete genome',\n",
+ " 'NZ_CP014322.1 Alteromonas addita strain R10SW13, complete genome',\n",
+ " 'NZ_CP014274.1 Stenotrophomonas sp. KCTC 12332, complete genome',\n",
+ " 'NZ_CP014323.1 Alteromonas macleodii strain D7, complete genome',\n",
+ " 'NZ_CP014301.1 Bosea sp. PAMC 26642, complete genome',\n",
+ " 'NZ_CP014302.1 Bosea sp. PAMC 26642 plasmid, complete sequence',\n",
+ " 'NZ_CP014304.1 Hymenobacter sp. PAMC26628, complete genome',\n",
+ " 'NZ_CP014303.1 Hymenobacter sp. PAMC26628 plasmid, complete sequence',\n",
+ " 'NZ_CP013928.1 Alteromonas mediterranea strain UM8, complete genome',\n",
+ " 'NZ_CP013929.1 Alteromonas mediterranea strain UM8 plasmid pAMEDUM8_300, complete sequence',\n",
+ " 'NZ_CP014206.1 Pseudodesulfovibrio indicus strain J2 chromosome, complete genome',\n",
+ " 'NZ_CP005083.1 Sphingobium sp. TKS chromosome 1, complete sequence',\n",
+ " 'NZ_CP005084.1 Sphingobium sp. TKS chromosome 2, complete sequence',\n",
+ " 'NZ_CP005085.1 Sphingobium sp. TKS plasmid pTK1, complete sequence',\n",
+ " 'NZ_CP005086.1 Sphingobium sp. TKS plasmid pTK2, complete sequence',\n",
+ " 'NZ_CP005087.1 Sphingobium sp. TKS plasmid pTK3, complete sequence',\n",
+ " 'NZ_CP005088.1 Sphingobium sp. TKS plasmid pTK4, complete sequence',\n",
+ " 'NZ_CP005090.1 Sphingobium sp. TKS plasmid pTK6, complete sequence',\n",
+ " 'NZ_CP005091.1 Sphingobium sp. TKS plasmid pTK7, complete sequence',\n",
+ " 'NZ_CP005092.1 Sphingobium sp. TKS plasmid pTK8, complete sequence',\n",
+ " 'NZ_CP005093.1 Sphingobium sp. TKS plasmid pTK9, complete sequence',\n",
+ " 'NZ_CP005089.1 Sphingobium sp. TKS plasmid pTK5, complete sequence',\n",
+ " 'NZ_CP005188.1 Sphingobium sp. MI1205 chromosome 1, complete sequence',\n",
+ " 'NZ_CP005189.1 Sphingobium sp. MI1205 chromosome 2, complete sequence',\n",
+ " 'NZ_CP005190.1 Sphingobium sp. MI1205 plasmid pMI1, complete sequence',\n",
+ " 'NZ_CP005191.1 Sphingobium sp. MI1205 plasmid pMI2, complete sequence',\n",
+ " 'NZ_CP005192.1 Sphingobium sp. MI1205 plasmid pMI3, complete sequence',\n",
+ " 'NZ_CP005193.1 Sphingobium sp. MI1205 plasmid pMI4, complete sequence',\n",
+ " 'NZ_CP014004.1 Klebsiella pneumoniae subsp. pneumoniae strain NUHL24835, complete genome',\n",
+ " 'NZ_CP014005.1 Klebsiella pneumoniae subsp. pneumoniae strain NUHL24835 plasmid unnamed1, complete sequence',\n",
+ " 'NZ_CP014006.1 Klebsiella pneumoniae subsp. pneumoniae strain NUHL24835 plasmid unnamed2, complete sequence',\n",
+ " 'NZ_CP013357.1 Burkholderia oklahomensis EO147 chromosome 1, complete sequence',\n",
+ " 'NZ_CP013356.1 Burkholderia oklahomensis EO147 chromosome 2, complete sequence',\n",
+ " 'NZ_CP013358.1 Burkholderia oklahomensis C6786 chromosome 1, complete sequence',\n",
+ " 'NZ_CP013359.1 Burkholderia oklahomensis C6786 chromosome 2, complete sequence',\n",
+ " 'NZ_CP013373.1 Burkholderia sp. NRF60-BP8 chromosome 1, complete sequence',\n",
+ " 'NZ_CP013372.1 Burkholderia sp. NRF60-BP8 chromosome 2, complete sequence',\n",
+ " 'NZ_CP013374.1 Burkholderia sp. NRF60-BP8 chromosome 3, complete sequence',\n",
+ " 'NZ_CP013389.1 Burkholderia sp. BDU8 chromosome 1, complete sequence',\n",
+ " 'NZ_CP013388.1 Burkholderia sp. BDU8 chromosome 2, complete sequence',\n",
+ " 'NZ_CP013386.1 Burkholderia sp. BDU6 chromosome 1, complete sequence',\n",
+ " 'NZ_CP013387.1 Burkholderia sp. BDU6 chromosome 2, complete sequence',\n",
+ " 'NZ_CP013384.1 Burkholderia sp. LA-2-3-30-S1-D2 chromosome 1, complete sequence',\n",
+ " 'NZ_CP013383.1 Burkholderia sp. LA-2-3-30-S1-D2 chromosome 2, complete sequence',\n",
+ " 'NZ_CP013385.1 Burkholderia sp. LA-2-3-30-S1-D2 chromosome 3, complete sequence',\n",
+ " 'NZ_CP013417.1 Burkholderia sp. MSMB0266 chromosome 1, complete sequence',\n",
+ " 'NZ_CP013418.1 Burkholderia sp. MSMB0266 chromosome 2, complete sequence',\n",
+ " 'NZ_CP013419.1 Burkholderia sp. MSMB0266 plasmid pMSMB0266, complete sequence',\n",
+ " 'NZ_CP013424.1 Burkholderia sp. MSMB0852 chromosome 1, complete sequence',\n",
+ " 'NZ_CP013425.1 Burkholderia sp. MSMB0852 chromosome 2, complete sequence',\n",
+ " 'NZ_CP013423.1 Burkholderia sp. MSMB0852 plasmid pMSMB0852, complete sequence',\n",
+ " 'NZ_CP013427.1 Burkholderia sp. MSMB0856 chromosome 1, complete sequence',\n",
+ " 'NZ_CP013428.1 Burkholderia sp. MSMB0856 chromosome 2, complete sequence',\n",
+ " 'NZ_CP013429.1 Burkholderia sp. MSMB0856 chromosome 3, complete sequence',\n",
+ " 'NZ_CP013426.1 Burkholderia sp. MSMB0856 plasmid pMSMB0856, complete sequence',\n",
+ " 'NZ_CP014010.1 Klebsiella pneumoniae subsp. pneumoniae strain RJF999, complete genome',\n",
+ " 'NZ_CP014011.1 Klebsiella pneumoniae subsp. pneumoniae strain RJF999 plasmid pRJF999, complete sequence',\n",
+ " 'NZ_CP014008.1 Klebsiella pneumoniae subsp. pneumoniae strain RJF293, complete genome',\n",
+ " 'NZ_CP014009.1 Klebsiella pneumoniae subsp. pneumoniae strain RJF293 plasmid pRJF293, complete sequence',\n",
+ " 'NZ_CP013457.1 Burkholderia sp. MSMB617WGS chromosome 1, complete sequence',\n",
+ " 'NZ_CP013458.1 Burkholderia sp. MSMB617WGS chromosome 2, complete sequence',\n",
+ " 'NZ_CP013992.1 Flavobacterium columnare strain 94-081, complete genome',\n",
+ " 'NZ_CP013920.1 Arsenophonus symbiont of Lipoptena fortisetosa strain CB, complete genome',\n",
+ " 'NZ_CP013975.1 Piscirickettsia salmonis strain CGR02, complete genome',\n",
+ " 'NZ_CP013976.1 Piscirickettsia salmonis strain CGR02 plasmid pPSCRG02-1, complete sequence',\n",
+ " 'NZ_CP013977.1 Piscirickettsia salmonis strain CGR02 plasmid pPSCRG02-2, complete sequence',\n",
+ " 'NZ_CP013978.1 Piscirickettsia salmonis strain CGR02 plasmid pPSCRG02-4, complete sequence',\n",
+ " 'NZ_CP013997.1 Pseudomonas monteilii strain USDA-ARS-USMARC-56711, complete genome',\n",
+ " 'NC_022998.1 Spiroplasma apis B31, complete genome',\n",
+ " 'NC_023037.2 Paenibacillus polymyxa CR1, complete genome',\n",
+ " 'NZ_CP006579.1 Aeromonas hydrophila 4AK4, complete genome',\n",
+ " 'NZ_CP006859.1 Listeria monocytogenes serotype 1/2a str. 08-6997, complete genome',\n",
+ " 'NZ_CP003915.1 Advenella mimigardefordensis DPN7, complete genome',\n",
+ " 'NZ_CP003916.1 Advenella mimigardefordensis DPN7 plasmid 24p, complete sequence',\n",
+ " 'NZ_CP007128.1 Gemmatirosa kalamazoonesis strain KBS708, complete genome',\n",
+ " 'NZ_CP007129.1 Gemmatirosa kalamazoonesis strain KBS708 plasmid 1, complete sequence',\n",
+ " 'NZ_CP007127.1 Gemmatirosa kalamazoonesis strain KBS708 phage-like extrachromosal element, complete sequence',\n",
+ " 'NZ_CP007130.1 Gemmatirosa kalamazoonesis strain KBS708 plasmid 2, complete sequence',\n",
+ " 'NZ_CP006720.1 Spiroplasma mirum ATCC 29335 strain SMCA, complete genome',\n",
+ " 'NZ_CP006715.1 Bifidobacterium breve 689b, complete genome',\n",
+ " 'NZ_CP007230.1 Yersinia similis strain 228, complete genome',\n",
+ " 'NZ_CP007231.1 Yersinia similis strain 228 plasmid, complete sequence',\n",
+ " 'NC_022107.1 Chlamydia trachomatis F/11-96, complete genome',\n",
+ " 'NZ_CP007446.1 Snodgrassella alvi wkB2, complete genome',\n",
+ " 'NZ_CP012371.1 Nitrosospira briensis C-128, complete genome',\n",
+ " 'NZ_CP010493.1 Campylobacter jejuni strain CJ677CC062, complete genome',\n",
+ " 'NZ_CP010494.1 Campylobacter jejuni strain CJ677CC059, complete genome',\n",
+ " 'NZ_CP010496.1 Campylobacter jejuni strain CJ677CC032, complete genome',\n",
+ " 'NZ_CP010497.1 Campylobacter jejuni strain CJ677CC033, complete genome',\n",
+ " 'NZ_CP010498.1 Campylobacter jejuni strain CJ677CC537, complete genome',\n",
+ " 'NZ_CP010499.1 Campylobacter jejuni strain CJ677CC542, complete genome',\n",
+ " 'NZ_CP010500.1 Campylobacter jejuni strain CJ677CC528, complete genome',\n",
+ " 'NZ_CP010495.1 Campylobacter jejuni strain CJ677CC538, complete genome',\n",
+ " 'NZ_CP010501.1 Campylobacter jejuni strain CJ677CC520, complete genome',\n",
+ " 'NZ_CP010502.1 Campylobacter jejuni strain CJ677CC014, complete genome',\n",
+ " 'NZ_CP010503.1 Campylobacter jejuni strain CJ677CC039, complete genome',\n",
+ " 'NZ_CP010504.1 Campylobacter jejuni strain CJ677CC085, complete genome',\n",
+ " 'NZ_CP010505.1 Campylobacter jejuni strain CJ677CC052, complete genome',\n",
+ " 'NZ_CP010506.1 Campylobacter jejuni strain CJ677CC527, complete genome',\n",
+ " 'NZ_CP010507.1 Campylobacter jejuni strain CJ677CC078, complete genome',\n",
+ " 'NZ_CP010508.1 Campylobacter jejuni strain CJ677CC523, complete genome',\n",
+ " 'NZ_CP010509.1 Campylobacter jejuni strain CJ677CC540, complete genome',\n",
+ " 'NZ_CP010510.1 Campylobacter jejuni strain CJ677CC040, complete genome',\n",
+ " 'NZ_CP010511.1 Campylobacter jejuni strain CJ677CC061, complete genome',\n",
+ " 'NZ_CP010457.1 Campylobacter jejuni strain CJ677CC539, complete genome',\n",
+ " 'NZ_CP010458.1 Campylobacter jejuni strain CJ677CC533, complete genome',\n",
+ " 'NZ_CP010459.1 Campylobacter jejuni strain CJ677CC047, complete genome',\n",
+ " 'NZ_CP009802.1 Streptomyces sp. FR-008, complete genome',\n",
+ " 'NZ_CP009803.1 Streptomyces sp. FR-008 plasmid pSSFR1, complete sequence',\n",
+ " 'NZ_CP009804.1 Streptomyces sp. FR-008 plasmid pSSFR2, complete sequence',\n",
+ " 'NZ_CP012482.1 Bacillus cellulasensis strain NJ-V2, complete genome',\n",
+ " 'NZ_CP013114.1 Staphylococcus equorum strain KS1039, complete genome',\n",
+ " 'NZ_CP009847.1 Vibrio parahaemolyticus strain FORC_004 chromosome 1, complete sequence',\n",
+ " 'NZ_CP009848.1 Vibrio parahaemolyticus strain FORC_004 chromosome 2, complete sequence',\n",
+ " 'NZ_CP009849.1 Vibrio parahaemolyticus strain FORC_004 plasmid pFORC4, complete sequence',\n",
+ " 'NZ_CP009984.1 Vibrio vulnificus strain FORC_009 chromosome 1, complete sequence',\n",
+ " 'NZ_CP009985.1 Vibrio vulnificus strain FORC_009 chromosome 2, complete sequence',\n",
+ " 'NZ_CP012837.1 Corynebacterium pseudotuberculosis strain 1002B, complete genome',\n",
+ " 'NZ_CP012907.1 Helicobacter pylori strain 29CaP, complete genome',\n",
+ " 'NZ_CP012905.1 Helicobacter pylori strain 7C, complete sequence',\n",
+ " 'NZ_CP012906.1 Helicobacter pylori strain 7C plasmid, complete sequence',\n",
+ " 'NZ_CP013120.1 Alteromonas stellipolaris LMG 21856, complete genome',\n",
+ " 'NZ_CP013121.1 Fusobacterium nucleatum subsp. polymorphum strain ChDC F306, complete genome',\n",
+ " 'NZ_CP013122.1 Fusobacterium nucleatum subsp. polymorphum strain ChDC F306 plasmid unnamed1, complete sequence',\n",
+ " 'NZ_CP013123.1 Fusobacterium nucleatum subsp. polymorphum strain ChDC F306 plasmid unnamed2, complete sequence',\n",
+ " 'NZ_CP014140.1 Aneurinibacillus sp. XH2, complete genome',\n",
+ " 'NZ_CP013126.1 Acidipropionibacterium acidipropionici strain CGMCC 1.2230 chromosome, complete genome',\n",
+ " 'NZ_CP012921.1 Salmonella enterica subsp. enterica serovar Heidelberg strain SA02DT10168701, complete genome',\n",
+ " 'NZ_CP012922.1 Salmonella enterica subsp. enterica serovar Heidelberg strain SA02DT10168701 plasmid pSA02DT10168701_37, complete sequence',\n",
+ " 'NZ_CP012923.1 Salmonella enterica subsp. enterica serovar Heidelberg strain SA02DT10168701 plasmid pSA02DT10168701_99, complete sequence',\n",
+ " 'NZ_CP012924.1 Salmonella enterica subsp. enterica serovar Heidelberg strain 12-4374, complete genome',\n",
+ " 'NZ_CP012925.1 Salmonella enterica subsp. enterica serovar Heidelberg strain 12-4374 plasmid p12-4374_2, complete sequence',\n",
+ " 'NZ_CP012927.1 Salmonella enterica subsp. enterica serovar Heidelberg strain 12-4374 plasmid p12-4374_3, complete sequence',\n",
+ " 'NZ_CP012926.1 Salmonella enterica subsp. enterica serovar Heidelberg strain 12-4374 plasmid p12-4374_37, complete sequence',\n",
+ " 'NZ_CP012928.1 Salmonella enterica subsp. enterica serovar Heidelberg strain 12-4374 plasmid p12-4374_62, complete sequence',\n",
+ " 'NZ_CP012929.1 Salmonella enterica subsp. enterica serovar Heidelberg strain 12-4374 plasmid p12-4374_96, complete sequence',\n",
+ " 'NZ_CP012930.1 Salmonella enterica subsp. enterica serovar Heidelberg strain N13-01290, complete genome',\n",
+ " 'NZ_CP012932.1 Salmonella enterica subsp. enterica serovar Heidelberg strain N13-01290 plasmid pN13-01290_2, complete sequence',\n",
+ " 'NZ_CP012931.1 Salmonella enterica subsp. enterica serovar Heidelberg strain N13-01290 plasmid pN13-01290_23, complete sequence',\n",
+ " 'NZ_CP012933.1 Salmonella enterica subsp. enterica serovar Heidelberg strain N13-01290 plasmid pN13-01290_3-1, complete sequence',\n",
+ " 'NZ_CP012934.1 Salmonella enterica subsp. enterica serovar Heidelberg strain N13-01290 plasmid pN13-01290_3-2, complete sequence',\n",
+ " 'NZ_CP012935.1 Salmonella enterica subsp. enterica serovar Heidelberg strain N13-01290 plasmid pN13-01290_3-3, complete sequence',\n",
+ " 'NZ_CP012936.1 Salmonella enterica subsp. enterica serovar Heidelberg strain N13-01290 plasmid pN13-01290_98, complete sequence',\n",
+ " 'NZ_CP013133.1 Rickettsia rhipicephali strain HJ#5, complete genome',\n",
+ " 'NZ_CP013134.1 Rickettsia rhipicephali strain HJ#5 plasmid pHJ51, complete sequence',\n",
+ " 'NZ_CP013135.1 Rickettsia rhipicephali strain HJ#5 plasmid pHJ52 sequence',\n",
+ " 'NZ_CP013112.1 Escherichia coli strain YD786, complete genome',\n",
+ " 'NZ_CP013141.1 Lysobacter antibioticus strain ATCC 29479 genome',\n",
+ " 'NZ_CP011129.1 Lysobacter antibioticus strain 76, complete genome',\n",
+ " 'NZ_CP012096.1 Serratia plymuthica strain 3Rp8, complete genome',\n",
+ " 'NZ_CP012097.1 Serratia plymuthica strain 3Re4-18, complete genome',\n",
+ " 'NZ_CP015963.1 Altererythrobacter ishigakiensis strain NBRC 107699 chromosome, complete genome',\n",
+ " 'NZ_CP016033.1 Porphyrobacter neustonensis strain DSM 9434, complete genome',\n",
+ " 'NZ_CP015990.1 Klebsiella pneumoniae strain BR chromosome, complete genome',\n",
+ " 'NZ_CP015991.1 Klebsiella pneumoniae strain BR plasmid pWSZBR, complete sequence',\n",
+ " 'NZ_CP014762.1 Klebsiella pneumoniae strain KPNIH39, complete genome',\n",
+ " 'NZ_CP014763.1 Klebsiella pneumoniae strain KPNIH39 plasmid pKPN-332, complete sequence',\n",
+ " 'NZ_CP014764.1 Klebsiella pneumoniae strain KPNIH39 plasmid pKPN-704, complete sequence',\n",
+ " 'NZ_CP014765.1 Klebsiella pneumoniae strain KPNIH39 plasmid pKpQIL-9b8, complete sequence',\n",
+ " 'NZ_CP012968.1 Staphylococcus sp. AntiMn-1, complete genome',\n",
+ " 'NZ_CP013300.1 Staphylococcus sp. AntiMn-1 plasmid AM1_232, complete sequence',\n",
+ " 'NZ_CP015850.1 Ralstonia solanacearum strain YC40-M chromosome, complete genome',\n",
+ " 'NZ_CP015851.1 Ralstonia solanacearum strain YC40-M plasmid, complete sequence',\n",
+ " 'NZ_CP015025.1 Klebsiella pneumoniae strain Kpn223, complete genome',\n",
+ " 'NZ_CP015026.1 Klebsiella pneumoniae strain Kpn223 plasmid pKPN-065, complete sequence',\n",
+ " 'NZ_CP015130.1 Klebsiella pneumoniae strain Kpn555 chromosome, complete genome',\n",
+ " 'NZ_CP015131.1 Klebsiella pneumoniae strain Kpn555 plasmid pKPN-7c3, complete sequence',\n",
+ " 'NZ_CP015133.1 Klebsiella pneumoniae strain Kpn555 plasmid pKPN-d6b, complete sequence',\n",
+ " 'NZ_CP015132.1 Klebsiella pneumoniae strain Kpn555 plasmid pKPN-d90, complete sequence',\n",
+ " 'NZ_CP015159.1 Escherichia coli strain Eco889 chromosome, complete genome',\n",
+ " 'NZ_CP015161.1 Escherichia coli strain Eco889 plasmid pECO-93a, complete sequence',\n",
+ " 'NZ_CP015160.1 Escherichia coli strain Eco889 plasmid pECO-fce, complete sequence',\n",
+ " 'NZ_CP015309.1 Corynebacterium pseudotuberculosis strain PA02 chromosome, complete genome',\n",
+ " 'NZ_CP014623.1 Lactobacillus backii strain TMW 1.1988 chromosome, complete genome',\n",
+ " 'NZ_CP014624.1 Lactobacillus backii strain TMW 1.1988 plasmid L11988-1, complete sequence',\n",
+ " 'NZ_CP014625.1 Lactobacillus backii strain TMW 1.1988 plasmid L11988-10, complete sequence',\n",
+ " 'NZ_CP014626.1 Lactobacillus backii strain TMW 1.1988 plasmid L11988-2, complete sequence',\n",
+ " 'NZ_CP014627.1 Lactobacillus backii strain TMW 1.1988 plasmid L11988-3, complete sequence',\n",
+ " 'NZ_CP014628.1 Lactobacillus backii strain TMW 1.1988 plasmid L11988-4, complete sequence',\n",
+ " 'NZ_CP014629.1 Lactobacillus backii strain TMW 1.1988 plasmid L11988-5, complete sequence',\n",
+ " 'NZ_CP014630.1 Lactobacillus backii strain TMW 1.1988 plasmid L11988-6, complete sequence',\n",
+ " 'NZ_CP014631.1 Lactobacillus backii strain TMW 1.1988 plasmid L11988-7, complete sequence',\n",
+ " 'NZ_CP014632.1 Lactobacillus backii strain TMW 1.1988 plasmid L11988-8, complete sequence',\n",
+ " 'NZ_CP014633.1 Lactobacillus backii strain TMW 1.1988 plasmid L11988-9, complete sequence',\n",
+ " 'NZ_CP012969.1 Psychrobacter sp. AntiMn-1, complete genome',\n",
+ " 'NZ_CP013101.1 Clostridium perfringens strain FORC_025, complete genome',\n",
+ " 'NZ_CP017715.1 Marinobacter salinus strain Hb8 chromosome, complete genome',\n",
+ " 'NZ_CP017188.2 Xanthomonas citri pv. glycines str. 8ra chromosome, complete genome',\n",
+ " 'NZ_CP017189.2 Xanthomonas citri pv. glycines str. 8ra plasmid pXAG27.8ra, complete sequence',\n",
+ " 'NZ_CP017190.1 Xanthomonas campestris pv. vesicatoria str. 85-10, complete sequence',\n",
+ " 'NZ_CP017191.1 Xanthomonas campestris pv. vesicatoria str. 85-10 plasmid p_XCV_1, complete sequence',\n",
+ " 'NZ_CP017192.1 Xanthomonas campestris pv. vesicatoria str. 85-10 plasmid p_XCV_2, complete sequence',\n",
+ " 'NZ_CP017193.1 Xanthomonas campestris pv. vesicatoria str. 85-10 plasmid p_XCV_3, complete sequence',\n",
+ " 'NZ_CP017603.1 Clostridium formicaceticum strain ATCC 27076, complete genome',\n",
+ " 'NZ_CP015208.1 Candidatus Rhodoluna planktonica strain MWH-Dar1, complete genome',\n",
+ " 'NZ_CP015381.1 Desulfococcus multivorans strain DSM 2059, complete genome',\n",
+ " 'NZ_CP017751.1 Cupriavidus sp. USMAHM13 chromosome 1, complete sequence',\n",
+ " 'NZ_CP017752.1 Cupriavidus sp. USMAHM13 chromosome 2, complete sequence',\n",
+ " 'NZ_CP017753.1 Cupriavidus sp. USMAHM13 plasmid unnamed1, complete sequence',\n",
+ " 'NZ_CP017748.1 Cupriavidus sp. USMAA2-4 chromosome 1, complete sequence',\n",
+ " 'NZ_CP017749.1 Cupriavidus sp. USMAA2-4 chromosome 2, complete sequence',\n",
+ " 'NZ_CP017750.1 Cupriavidus sp. USMAA2-4 plasmid unnamed1, complete sequence',\n",
+ " 'NZ_CP017754.1 Cupriavidus sp. USMAA1020 chromosome 1, complete sequence',\n",
+ " 'NZ_CP017755.1 Cupriavidus sp. USMAA1020 chromosome 2, complete sequence',\n",
+ " 'NZ_CP017756.1 Cupriavidus sp. USMAA1020 plasmid unnamed1, complete sequence',\n",
+ " 'NZ_CP017747.1 Bacillus velezensis strain SYBC H47 chromosome, complete genome',\n",
+ " 'NZ_CP017421.1 Arthrobacter sp. ZXY-2 chromosome, complete genome',\n",
+ " 'NZ_CP017422.1 Arthrobacter sp. ZXY-2 plasmid pZXY21, complete sequence',\n",
+ " 'NZ_CP017423.1 Arthrobacter sp. ZXY-2 plasmid pZXY22, complete sequence',\n",
+ " 'NZ_CP017424.1 Arthrobacter sp. ZXY-2 plasmid pZXY23, complete sequence',\n",
+ " 'NZ_CP017425.1 Arthrobacter sp. ZXY-2 plasmid pZXY24, complete sequence',\n",
+ " 'NZ_CP017426.1 Arthrobacter sp. ZXY-2 plasmid pZXY25, complete sequence',\n",
+ " 'NZ_CP017640.1 Methylobacterium sp. C1 chromosome, complete genome',\n",
+ " 'NZ_CP017718.1 Hyphomonas sp. Mor2 genome',\n",
+ " 'NZ_CP013013.1 Vibrio cholerae strain Env-390 chromosome 1, complete sequence',\n",
+ " 'NZ_CP013014.1 Vibrio cholerae strain Env-390 chromosome 2, complete sequence',\n",
+ " 'NZ_CP013475.1 Mycobacterium tuberculosis strain 1458, complete genome',\n",
+ " 'NZ_CP017707.1 Chromobacterium vaccinii strain 21-1 chromosome, complete genome',\n",
+ " 'NZ_CP017622.1 Ketogulonicigenium vulgare strain SPU B805 chromosome, complete genome',\n",
+ " 'NZ_CP012426.1 Klebsiella pneumoniae strain KP5 chromosome, complete genome',\n",
+ " 'NZ_CP012427.1 Klebsiella pneumoniae strain KP5 plasmid pSg1-1, complete sequence',\n",
+ " 'NZ_CP012428.1 Klebsiella pneumoniae strain KP5 plasmid pSg1-2, complete sequence',\n",
+ " 'NZ_CP012429.1 Klebsiella pneumoniae strain KP5 plasmid pSg1-3, complete sequence',\n",
+ " 'NZ_CP011839.1 Klebsiella pneumoniae strain KP5 plasmid pSg1-NDM, complete sequence',\n",
+ " 'NZ_CP017100.1 Escherichia coli strain K-12 NEB 5-alpha chromosome, complete genome',\n",
+ " 'NZ_CP017107.1 Lactobacillus salivarius strain CICC 23174 chromosome, complete genome',\n",
+ " 'NZ_CP017108.1 Lactobacillus salivarius strain CICC23174 plasmid pLS_1 sequence',\n",
+ " 'NZ_CP017109.1 Lactobacillus salivarius strain CICC23174 plasmid pLS_2 sequence',\n",
+ " 'NZ_CP017110.1 Lactobacillus salivarius strain CICC23174 plasmid pLS_3, complete sequence',\n",
+ " 'NZ_CP017124.1 Lactobacillus curvatus strain WiKim38, complete genome',\n",
+ " 'NZ_CP016395.1 Bacillus velezensis strain M75 chromosome, complete genome',\n",
+ " 'NZ_CP017111.1 Sulfurospirillum halorespirans DSM 13726 chromosome, complete genome',\n",
+ " 'NZ_CP017116.1 Erysipelothrix rhusiopathiae strain WH13013 chromosome, complete genome',\n",
+ " 'NZ_CP012692.1 Staphylococcus aureus strain FORC_027, complete genome',\n",
+ " 'NZ_CP016019.1 Bifidobacterium longum subsp. longum strain AH1206, complete genome',\n",
+ " 'NZ_CP017247.1 Bacillus licheniformis strain BL1202, complete genome',\n",
+ " 'NZ_CP016385.1 Salmonella enterica subsp. enterica serovar Typhimurium strain 13-931, complete genome',\n",
+ " 'NZ_CP016386.1 Salmonella enterica subsp. enterica serovar Typhimurium strain 13-931 plasmid p931-3904, complete sequence',\n",
+ " 'NZ_CP016387.1 Salmonella enterica subsp. enterica serovar Typhimurium strain 13-931 plasmid p931IncI1, complete sequence',\n",
+ " 'NZ_CP016388.1 Salmonella enterica subsp. enterica serovar Typhimurium strain 13-931 plasmid p931IncI2, complete sequence',\n",
+ " 'NZ_CP016389.1 Salmonella enterica subsp. enterica serovar Typhimurium strain 13-931 plasmid pESBL931, complete sequence',\n",
+ " 'NZ_CP016390.1 Salmonella enterica subsp. enterica serovar Typhimurium strain 13-931 plasmid pSLT931, complete sequence',\n",
+ " 'NZ_CP015217.1 Leptospira alstonii strain GWTS #1 chromosome 1, complete sequence',\n",
+ " 'NZ_CP015218.1 Leptospira alstonii strain GWTS #1 chromosome 2, complete sequence',\n",
+ " 'NZ_CP016044.1 Edwardsiella piscicida strain S11-285 chromosome, complete genome',\n",
+ " 'NZ_CP016445.1 Edwardsiella piscicida strain S11-285 plasmid unnamed1, complete sequence',\n",
+ " 'NZ_CP017157.1 Streptomyces lydicus strain 103 chromosome, complete genome',\n",
+ " 'NZ_CP017149.1 Pseudomonas aeruginosa strain ATCC 15692 chromosome, complete genome',\n",
+ " 'NZ_CP017150.1 Brevibacterium aurantiacum strain SMQ-1335 chromosome, complete genome',\n",
+ " 'NZ_CP017175.1 Burkholderia mallei strain Bahrain1 chromosome 1, complete sequence',\n",
+ " 'NZ_CP017176.1 Burkholderia mallei strain Bahrain1 chromosome 2, complete sequence',\n",
+ " 'NZ_CP016894.1 Bacillus subtilis strain HJ0-6, complete genome',\n",
+ " 'NZ_CP016895.1 Acinetobacter larvae strain BRTC-1 chromosome, complete genome',\n",
+ " 'NZ_CP016294.1 Stenotrophomonas rhizophila strain QL-P4, complete genome',\n",
+ " 'NZ_CP016824.1 Streptomyces sampsonii strain KJ40 chromosome, complete genome',\n",
+ " 'NZ_CP016341.1 Bordetella holmesii strain H903, complete genome',\n",
+ " 'NZ_CP016811.1 Klebsiella pneumoniae strain DHQP1002001 chromosome, complete genome',\n",
+ " 'NZ_CP016810.1 Klebsiella pneumoniae strain DHQP1002001 plasmid p_IncFIB_DHQP1002001, complete sequence',\n",
+ " 'NZ_CP016812.1 Klebsiella pneumoniae strain DHQP1002001 plasmid p_incR_DHQP1002001, complete sequence',\n",
+ " 'NZ_CP016342.1 Bordetella parapertussis strain H904, complete genome',\n",
+ " 'NZ_CP011533.1 Streptomyces noursei ATCC 11455, complete genome',\n",
+ " 'NZ_CP012334.1 Bordetella sp. H567, complete genome',\n",
+ " 'NZ_CP013749.1 Lactobacillus plantarum strain KP, complete genome',\n",
+ " 'NZ_CP013750.1 Lactobacillus plantarum strain KP plasmid unnamed1, complete sequence',\n",
+ " 'NZ_CP013751.1 Lactobacillus plantarum strain KP plasmid unnamed2, complete sequence',\n",
+ " 'NZ_CP013752.1 Lactobacillus plantarum strain KP plasmid unnamed3, complete sequence',\n",
+ " 'NZ_CP013753.1 Lactobacillus plantarum strain DF, complete genome',\n",
+ " 'NZ_CP013754.1 Lactobacillus plantarum strain DF plasmid unnamed1, complete sequence',\n",
+ " 'NZ_CP013755.1 Lactobacillus plantarum strain DF plasmid unnamed2, complete sequence',\n",
+ " 'NZ_CP013756.1 Lactobacillus plantarum strain DF plasmid unnamed3, complete sequence',\n",
+ " 'NZ_CP016431.1 Bordetella bronchiseptica strain I328 chromosome, complete genome',\n",
+ " 'NZ_CP029397.1 Acinetobacter defluvii strain WCHA30 chromosome, complete genome',\n",
+ " 'NZ_CP029389.1 Acinetobacter defluvii strain WCHA30 plasmid p1_010030, complete sequence',\n",
+ " 'NZ_CP029390.1 Acinetobacter defluvii strain WCHA30 plasmid p2_010030, complete sequence',\n",
+ " 'NZ_CP029391.1 Acinetobacter defluvii strain WCHA30 plasmid p3_010030, complete sequence',\n",
+ " 'NZ_CP029392.1 Acinetobacter defluvii strain WCHA30 plasmid p4_010030, complete sequence',\n",
+ " 'NZ_CP029393.1 Acinetobacter defluvii strain WCHA30 plasmid p5_010030, complete sequence',\n",
+ " 'NZ_CP029394.1 Acinetobacter defluvii strain WCHA30 plasmid p6_010030, complete sequence',\n",
+ " 'NZ_CP029395.1 Acinetobacter defluvii strain WCHA30 plasmid p7_010030, complete sequence',\n",
+ " 'NZ_CP029396.1 Acinetobacter defluvii strain WCHA30 plasmid pOXA58_010030, complete sequence',\n",
+ " 'NZ_CP012375.1 Microcystis aeruginosa NIES-2481, complete genome',\n",
+ " 'NZ_CP025929.1 Microcystis aeruginosa NIES-2481 plasmid p1, complete sequence',\n",
+ " ...]"
+ ]
+ },
+ "execution_count": 25,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "all_fastas"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 117,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<div>\n",
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+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>n_sequences</th>\n",
+ " <th>species</th>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>genus</th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>Bacillus</th>\n",
+ " <td>1132</td>\n",
+ " <td>11</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Streptomyces</th>\n",
+ " <td>743</td>\n",
+ " <td>5</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Vibrio</th>\n",
+ " <td>468</td>\n",
+ " <td>5</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Rhizobium</th>\n",
+ " <td>325</td>\n",
+ " <td>6</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Pseudomonas</th>\n",
+ " <td>304</td>\n",
+ " <td>8</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Staphylococcus</th>\n",
+ " <td>301</td>\n",
+ " <td>6</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Clostridium</th>\n",
+ " <td>259</td>\n",
+ " <td>5</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Streptococcus</th>\n",
+ " <td>222</td>\n",
+ " <td>6</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Planktothrix</th>\n",
+ " <td>179</td>\n",
+ " <td>5</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Stenotrophomonas</th>\n",
+ " <td>176</td>\n",
+ " <td>5</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Escherichia</th>\n",
+ " <td>133</td>\n",
+ " <td>3</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Paenibacillus</th>\n",
+ " <td>127</td>\n",
+ " <td>3</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Listeria</th>\n",
+ " <td>104</td>\n",
+ " <td>4</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Corynebacterium</th>\n",
+ " <td>103</td>\n",
+ " <td>7</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Klebsiella</th>\n",
+ " <td>16</td>\n",
+ " <td>3</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Shigella</th>\n",
+ " <td>14</td>\n",
+ " <td>3</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Salmonella</th>\n",
+ " <td>4</td>\n",
+ " <td>2</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Enterobacter</th>\n",
+ " <td>1</td>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
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+ " n_sequences species\n",
+ "genus \n",
+ "Bacillus 1132 11\n",
+ "Streptomyces 743 5\n",
+ "Vibrio 468 5\n",
+ "Rhizobium 325 6\n",
+ "Pseudomonas 304 8\n",
+ "Staphylococcus 301 6\n",
+ "Clostridium 259 5\n",
+ "Streptococcus 222 6\n",
+ "Planktothrix 179 5\n",
+ "Stenotrophomonas 176 5\n",
+ "Escherichia 133 3\n",
+ "Paenibacillus 127 3\n",
+ "Listeria 104 4\n",
+ "Corynebacterium 103 7\n",
+ "Klebsiella 16 3\n",
+ "Shigella 14 3\n",
+ "Salmonella 4 2\n",
+ "Enterobacter 1 1"
+ ]
+ },
+ "execution_count": 117,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "counts = inventory.reset_index().groupby(\"genus\").agg({\"count\", sum}).drop((\"species\"), axis=1)\n",
+ "counts.columns=[\"n_sequences\",\"species\"]\n",
+ "counts.sort_values(\"n_sequences\", ascending=False)"
+ ]
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