parse_pfam_index.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Populating the interactive namespace from numpy and matplotlib\n"
     ]
    }
   ],
   "source": [
    "from  bs4 import BeautifulSoup\n",
    "import pandas as pd\n",
    "import requests\n",
    "%pylab inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "5879\n"
     ]
    }
   ],
   "source": [
    "## ad-hoc clusterfuck of a parsing of the pfam species summary table \n",
    "## from http://pfam.xfam.org/proteome/browse\n",
    "## (actually works)\n",
    "\n",
    "pfam_index = requests.get('http://pfam.xfam.org/proteome/browse')\n",
    "\n",
    "soup = BeautifulSoup(pfam_index.text, \"html.parser\")\n",
    "\n",
    "tables = soup.find_all(name='table')\n",
    "\n",
    "samples = tables[1]\n",
    "\n",
    "rows = [row for row in samples.children]\n",
    "\n",
    "rows = rows[3]\n",
    "\n",
    "rows = list(filter(lambda x: x!='\\n', rows))\n",
    "\n",
    "print(len(rows))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pfam_id</th>\n",
       "      <th>kingdom</th>\n",
       "      <th>proteome_size</th>\n",
       "      <th>seq_cov</th>\n",
       "      <th>res_cov</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>'Deinococcus soli' Cha et al. 2014</th>\n",
       "      <td>1309411</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>2935</td>\n",
       "      <td>79</td>\n",
       "      <td>60</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>'Echinacea purpurea' witches'-broom phytoplasma</th>\n",
       "      <td>1123738</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>433</td>\n",
       "      <td>75</td>\n",
       "      <td>58</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Abalone herpesvirus (isolate Abalone/Australia/Victoria/2009) (AbHV)</th>\n",
       "      <td>1241371</td>\n",
       "      <td>Viruses</td>\n",
       "      <td>112</td>\n",
       "      <td>16</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Abiotrophia defectiva ATCC 49176</th>\n",
       "      <td>592010</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>1943</td>\n",
       "      <td>81</td>\n",
       "      <td>62</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acanthamoeba castellanii str. Neff</th>\n",
       "      <td>1257118</td>\n",
       "      <td>Eukaryota</td>\n",
       "      <td>14939</td>\n",
       "      <td>65</td>\n",
       "      <td>35</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acanthamoeba polyphaga mimivirus (APMV)</th>\n",
       "      <td>212035</td>\n",
       "      <td>Viruses</td>\n",
       "      <td>909</td>\n",
       "      <td>42</td>\n",
       "      <td>27</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acanthisitta chloris (rifleman)</th>\n",
       "      <td>57068</td>\n",
       "      <td>Eukaryota</td>\n",
       "      <td>9650</td>\n",
       "      <td>84</td>\n",
       "      <td>50</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acaryochloris marina (strain MBIC 11017)</th>\n",
       "      <td>329726</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>8172</td>\n",
       "      <td>61</td>\n",
       "      <td>51</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Accumulibacter phosphatis (strain UW-1)</th>\n",
       "      <td>522306</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>4438</td>\n",
       "      <td>83</td>\n",
       "      <td>59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Acetivibrio ethanolgignens</th>\n",
       "      <td>290052</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>3375</td>\n",
       "      <td>75</td>\n",
       "      <td>56</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    pfam_id    kingdom  \\\n",
       "'Deinococcus soli' Cha et al. 2014                  1309411   Bacteria   \n",
       "'Echinacea purpurea' witches'-broom phytoplasma     1123738   Bacteria   \n",
       "Abalone herpesvirus (isolate Abalone/Australia/...  1241371    Viruses   \n",
       "Abiotrophia defectiva ATCC 49176                     592010   Bacteria   \n",
       "Acanthamoeba castellanii str. Neff                  1257118  Eukaryota   \n",
       "Acanthamoeba polyphaga mimivirus (APMV)              212035    Viruses   \n",
       "Acanthisitta chloris (rifleman)                       57068  Eukaryota   \n",
       "Acaryochloris marina (strain MBIC 11017)             329726   Bacteria   \n",
       "Accumulibacter phosphatis (strain UW-1)              522306   Bacteria   \n",
       "Acetivibrio ethanolgignens                           290052   Bacteria   \n",
       "\n",
       "                                                    proteome_size  seq_cov  \\\n",
       "'Deinococcus soli' Cha et al. 2014                           2935       79   \n",
       "'Echinacea purpurea' witches'-broom phytoplasma               433       75   \n",
       "Abalone herpesvirus (isolate Abalone/Australia/...            112       16   \n",
       "Abiotrophia defectiva ATCC 49176                             1943       81   \n",
       "Acanthamoeba castellanii str. Neff                          14939       65   \n",
       "Acanthamoeba polyphaga mimivirus (APMV)                       909       42   \n",
       "Acanthisitta chloris (rifleman)                              9650       84   \n",
       "Acaryochloris marina (strain MBIC 11017)                     8172       61   \n",
       "Accumulibacter phosphatis (strain UW-1)                      4438       83   \n",
       "Acetivibrio ethanolgignens                                   3375       75   \n",
       "\n",
       "                                                    res_cov  \n",
       "'Deinococcus soli' Cha et al. 2014                       60  \n",
       "'Echinacea purpurea' witches'-broom phytoplasma          58  \n",
       "Abalone herpesvirus (isolate Abalone/Australia/...        8  \n",
       "Abiotrophia defectiva ATCC 49176                         62  \n",
       "Acanthamoeba castellanii str. Neff                       35  \n",
       "Acanthamoeba polyphaga mimivirus (APMV)                  27  \n",
       "Acanthisitta chloris (rifleman)                          50  \n",
       "Acaryochloris marina (strain MBIC 11017)                 51  \n",
       "Accumulibacter phosphatis (strain UW-1)                  59  \n",
       "Acetivibrio ethanolgignens                               56  "
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# parse rows into a dict\n",
    "data = dict()\n",
    "for tmp in rows : \n",
    "    \n",
    "    species = tmp.a.text\n",
    "    row = { 'pfam_id': tmp.a['href'].split('=')[-1],\n",
    "           'kingdom' : tmp.find_all('td')[1].text,\n",
    "           'proteome_size' : int(tmp.find_all('td')[2].text),\n",
    "           'seq_cov': int(tmp.find_all('td')[3].text),\n",
    "           'res_cov': int(tmp.find_all('td')[4].text)\n",
    "          }\n",
    "    data[species]=row\n",
    "    \n",
    "#finally parse into a dataframe\n",
    "data = pd.DataFrame.from_dict(data, orient='index')\n",
    "data.describe()\n",
    "data.head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 197,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "80.0"
      ]
     },
     "execution_count": 197,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAYgAAAEWCAYAAAB8LwAVAAAABHNCSVQICAgIfAhkiAAAAAlwSFlz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\nrkJggg==\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fcd940a7668>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#distribution of sequence coverage for bacteria\n",
    "isBacteria = data['kingdom'] == 'Bacteria'\n",
    "scov = data[isBacteria]['seq_cov']\n",
    "\n",
    "hist(scov, bins = range(min(scov), max(scov)));\n",
    "title('sequence coverage for bacteria')\n",
    "xlabel('coverage')\n",
    "ylabel('count')\n",
    "\n",
    "median(data[isBacteria]['seq_cov'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 200,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2729"
      ]
     },
     "execution_count": 200,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "threshold = 80\n",
    "\n",
    "covered = data['seq_cov'] >=threshold\n",
    "sum(covered)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 201,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "4391\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<matplotlib.text.Text at 0x7fcd7f5bb320>"
      ]
     },
     "execution_count": 201,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAYgAAAEWCAYAAAB8LwAVAAAABHNCSVQICAgIfAhkiAAAAAlwSFlz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\n3KG7FVnlAAAAAElFTkSuQmCC\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fcd653859b0>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "hist(data[isBacteria]['proteome_size'], bins = 100);\n",
    "print (len(data[isBacteria]))\n",
    "title('proteome size for bacteria')\n",
    "xlabel('proteome size')\n",
    "ylabel('count')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 164,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>pfam_id</th>\n",
       "      <th>kingdom</th>\n",
       "      <th>proteome_size</th>\n",
       "      <th>seq_cov</th>\n",
       "      <th>res_cov</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>'Echinacea purpurea' witches'-broom phytoplasma</th>\n",
       "      <td>1123738</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>433</td>\n",
       "      <td>75</td>\n",
       "      <td>58</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Actinobacteria bacterium BACL2 MAG-120920-bin34</th>\n",
       "      <td>1655602</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>999</td>\n",
       "      <td>88</td>\n",
       "      <td>69</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Actinobacteria bacterium BACL4 MAG-120813-bin39</th>\n",
       "      <td>1655578</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>499</td>\n",
       "      <td>92</td>\n",
       "      <td>73</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Amycolatopsis halophila YIM 93223</th>\n",
       "      <td>592678</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>356</td>\n",
       "      <td>79</td>\n",
       "      <td>58</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Anaerolineae bacterium 49_20</th>\n",
       "      <td>1641376</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>966</td>\n",
       "      <td>83</td>\n",
       "      <td>62</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Anaplasma marginale (strain Florida)</th>\n",
       "      <td>320483</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>938</td>\n",
       "      <td>80</td>\n",
       "      <td>55</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Arsenophonus symbiont of Lipoptena fortisetosa</th>\n",
       "      <td>634113</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>625</td>\n",
       "      <td>100</td>\n",
       "      <td>78</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Atribacteria bacterium 34_128</th>\n",
       "      <td>1635291</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>834</td>\n",
       "      <td>89</td>\n",
       "      <td>72</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Atribacteria bacterium 34_868</th>\n",
       "      <td>1641392</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>237</td>\n",
       "      <td>85</td>\n",
       "      <td>70</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Azobacteroides pseudotrichonymphae genomovar. CFP2</th>\n",
       "      <td>511995</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>847</td>\n",
       "      <td>86</td>\n",
       "      <td>68</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Baumannia cicadellinicola subsp. Homalodisca coagulata</th>\n",
       "      <td>374463</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>595</td>\n",
       "      <td>99</td>\n",
       "      <td>77</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Bifidobacterium pseudocatenulatum</th>\n",
       "      <td>28026</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>986</td>\n",
       "      <td>86</td>\n",
       "      <td>62</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Blattabacterium sp. (Cryptocercus punctulatus) str. Cpu</th>\n",
       "      <td>1075399</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>548</td>\n",
       "      <td>94</td>\n",
       "      <td>73</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Blochmannia endosymbiont of Camponotus (Colobopsis) obliquus</th>\n",
       "      <td>1505597</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>584</td>\n",
       "      <td>99</td>\n",
       "      <td>78</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Blochmannia endosymbiont of Polyrhachis (Hedomyrma) turneri</th>\n",
       "      <td>1505596</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>589</td>\n",
       "      <td>99</td>\n",
       "      <td>78</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Blochmannia floridanus</th>\n",
       "      <td>203907</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>583</td>\n",
       "      <td>100</td>\n",
       "      <td>78</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Borrelia turicatae (strain 91E135)</th>\n",
       "      <td>314724</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>818</td>\n",
       "      <td>82</td>\n",
       "      <td>58</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Buchnera aphidicola (Cinara tujafilina)</th>\n",
       "      <td>261317</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>359</td>\n",
       "      <td>98</td>\n",
       "      <td>78</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) (Acyrthosiphon pisum symbiotic bacterium)</th>\n",
       "      <td>107806</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>572</td>\n",
       "      <td>98</td>\n",
       "      <td>79</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)</th>\n",
       "      <td>224915</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>507</td>\n",
       "      <td>99</td>\n",
       "      <td>79</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Buchnera aphidicola subsp. Cinara cedri (strain Cc)</th>\n",
       "      <td>372461</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>362</td>\n",
       "      <td>98</td>\n",
       "      <td>78</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Buchnera aphidicola subsp. Schlechtendalia chinensis</th>\n",
       "      <td>118110</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>499</td>\n",
       "      <td>98</td>\n",
       "      <td>79</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Candidatus Baumannia cicadellinicola</th>\n",
       "      <td>186490</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>550</td>\n",
       "      <td>96</td>\n",
       "      <td>77</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Candidatus Carsonella ruddii DC</th>\n",
       "      <td>667013</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>206</td>\n",
       "      <td>75</td>\n",
       "      <td>67</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Candidatus Curtissbacteria bacterium GW2011_GWA1_40_24</th>\n",
       "      <td>1618406</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>280</td>\n",
       "      <td>76</td>\n",
       "      <td>60</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Candidatus Endolissoclinum faulkneri L5</th>\n",
       "      <td>1401328</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>770</td>\n",
       "      <td>98</td>\n",
       "      <td>74</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Candidatus Evansia muelleri</th>\n",
       "      <td>1495769</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>330</td>\n",
       "      <td>96</td>\n",
       "      <td>77</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Candidatus Gottesmanbacteria bacterium GW2011_GWA1_47_8</th>\n",
       "      <td>1618438</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>336</td>\n",
       "      <td>75</td>\n",
       "      <td>63</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Candidatus Hodgkinia cicadicola</th>\n",
       "      <td>573658</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>170</td>\n",
       "      <td>76</td>\n",
       "      <td>62</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Candidatus Ishikawaella capsulata Mpkobe</th>\n",
       "      <td>476281</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>623</td>\n",
       "      <td>97</td>\n",
       "      <td>79</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Parcubacteria group bacterium GW2011_GWA1_60_11</th>\n",
       "      <td>1618805</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>237</td>\n",
       "      <td>76</td>\n",
       "      <td>64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Parcubacteria group bacterium GW2011_GWB1_45_7</th>\n",
       "      <td>1618878</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>359</td>\n",
       "      <td>75</td>\n",
       "      <td>62</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Pelotomaculum thermopropionicum</th>\n",
       "      <td>110500</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>772</td>\n",
       "      <td>85</td>\n",
       "      <td>69</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Phytoplasma mali (strain AT)</th>\n",
       "      <td>482235</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>448</td>\n",
       "      <td>76</td>\n",
       "      <td>60</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Pseudomonas sp. 63_8</th>\n",
       "      <td>1641374</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>605</td>\n",
       "      <td>80</td>\n",
       "      <td>65</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Psychromonas sp. PRT-SC03</th>\n",
       "      <td>1527299</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>787</td>\n",
       "      <td>86</td>\n",
       "      <td>67</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Rhodobacteraceae bacterium HLUCCA09</th>\n",
       "      <td>1666915</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>634</td>\n",
       "      <td>85</td>\n",
       "      <td>64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Rhodobacteraceae bacterium HLUCCA24</th>\n",
       "      <td>1666918</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>537</td>\n",
       "      <td>78</td>\n",
       "      <td>65</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Rickettsia prowazekii (strain Madrid E)</th>\n",
       "      <td>272947</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>834</td>\n",
       "      <td>92</td>\n",
       "      <td>67</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Riesia pediculicola (strain USDA)</th>\n",
       "      <td>515618</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>540</td>\n",
       "      <td>84</td>\n",
       "      <td>77</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ruthia magnifica subsp. Calyptogena magnifica</th>\n",
       "      <td>413404</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>976</td>\n",
       "      <td>93</td>\n",
       "      <td>75</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>SAR11 cluster bacterium PRT-SC02</th>\n",
       "      <td>1527298</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>632</td>\n",
       "      <td>88</td>\n",
       "      <td>72</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Saccharibacillus sacchari DSM 19268</th>\n",
       "      <td>915437</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>299</td>\n",
       "      <td>90</td>\n",
       "      <td>67</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Serratia symbiotica str. 'Cinara cedri'</th>\n",
       "      <td>568817</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>672</td>\n",
       "      <td>100</td>\n",
       "      <td>77</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Sinorhizobium fredii GR64</th>\n",
       "      <td>882101</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>166</td>\n",
       "      <td>81</td>\n",
       "      <td>61</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Sulcia muelleri (strain GWSS)</th>\n",
       "      <td>444179</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>227</td>\n",
       "      <td>96</td>\n",
       "      <td>77</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Tropheryma whipplei (strain Twist) (Whipple's bacillus)</th>\n",
       "      <td>203267</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>805</td>\n",
       "      <td>84</td>\n",
       "      <td>64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Uncultured termite group 1 bacterium phylotype Rs-D17</th>\n",
       "      <td>471821</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>767</td>\n",
       "      <td>89</td>\n",
       "      <td>71</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Veillonella parvula</th>\n",
       "      <td>29466</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>923</td>\n",
       "      <td>83</td>\n",
       "      <td>64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Wigglesworthia glossinidia brevipalpis</th>\n",
       "      <td>36870</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>617</td>\n",
       "      <td>99</td>\n",
       "      <td>76</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Wolbachia endosymbiont of Onchocerca ochengi</th>\n",
       "      <td>100901</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>647</td>\n",
       "      <td>89</td>\n",
       "      <td>69</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Zinderia insecticola (strain CARI)</th>\n",
       "      <td>871271</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>206</td>\n",
       "      <td>95</td>\n",
       "      <td>76</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>actinobacterium acAMD-2</th>\n",
       "      <td>1504318</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>962</td>\n",
       "      <td>86</td>\n",
       "      <td>64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>actinobacterium acIB-AMD-6</th>\n",
       "      <td>1504321</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>551</td>\n",
       "      <td>92</td>\n",
       "      <td>73</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>actinobacterium acMicro-1</th>\n",
       "      <td>1504316</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>873</td>\n",
       "      <td>86</td>\n",
       "      <td>66</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>candidate division WWE3 bacterium GW2011_GWA2_44_16</th>\n",
       "      <td>1619110</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>365</td>\n",
       "      <td>76</td>\n",
       "      <td>53</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>candidate division WWE3 bacterium GW2011_GWA2_46_9</th>\n",
       "      <td>1619111</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>359</td>\n",
       "      <td>77</td>\n",
       "      <td>55</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>candidate division Zixibacteria bacterium DG_27</th>\n",
       "      <td>1703423</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>961</td>\n",
       "      <td>75</td>\n",
       "      <td>57</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>endosymbiont of Llaveia axin axin</th>\n",
       "      <td>1415657</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>242</td>\n",
       "      <td>99</td>\n",
       "      <td>77</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>secondary endosymbiont of Heteropsylla cubana</th>\n",
       "      <td>134287</td>\n",
       "      <td>Bacteria</td>\n",
       "      <td>576</td>\n",
       "      <td>94</td>\n",
       "      <td>77</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>106 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                    pfam_id   kingdom  \\\n",
       "'Echinacea purpurea' witches'-broom phytoplasma     1123738  Bacteria   \n",
       "Actinobacteria bacterium BACL2 MAG-120920-bin34     1655602  Bacteria   \n",
       "Actinobacteria bacterium BACL4 MAG-120813-bin39     1655578  Bacteria   \n",
       "Amycolatopsis halophila YIM 93223                    592678  Bacteria   \n",
       "Anaerolineae bacterium 49_20                        1641376  Bacteria   \n",
       "Anaplasma marginale (strain Florida)                 320483  Bacteria   \n",
       "Arsenophonus symbiont of Lipoptena fortisetosa       634113  Bacteria   \n",
       "Atribacteria bacterium 34_128                       1635291  Bacteria   \n",
       "Atribacteria bacterium 34_868                       1641392  Bacteria   \n",
       "Azobacteroides pseudotrichonymphae genomovar. CFP2   511995  Bacteria   \n",
       "Baumannia cicadellinicola subsp. Homalodisca co...   374463  Bacteria   \n",
       "Bifidobacterium pseudocatenulatum                     28026  Bacteria   \n",
       "Blattabacterium sp. (Cryptocercus punctulatus) ...  1075399  Bacteria   \n",
       "Blochmannia endosymbiont of Camponotus (Colobop...  1505597  Bacteria   \n",
       "Blochmannia endosymbiont of Polyrhachis (Hedomy...  1505596  Bacteria   \n",
       "Blochmannia floridanus                               203907  Bacteria   \n",
       "Borrelia turicatae (strain 91E135)                   314724  Bacteria   \n",
       "Buchnera aphidicola (Cinara tujafilina)              261317  Bacteria   \n",
       "Buchnera aphidicola subsp. Acyrthosiphon pisum ...   107806  Bacteria   \n",
       "Buchnera aphidicola subsp. Baizongia pistaciae ...   224915  Bacteria   \n",
       "Buchnera aphidicola subsp. Cinara cedri (strain...   372461  Bacteria   \n",
       "Buchnera aphidicola subsp. Schlechtendalia chin...   118110  Bacteria   \n",
       "Candidatus Baumannia cicadellinicola                 186490  Bacteria   \n",
       "Candidatus Carsonella ruddii DC                      667013  Bacteria   \n",
       "Candidatus Curtissbacteria bacterium GW2011_GWA...  1618406  Bacteria   \n",
       "Candidatus Endolissoclinum faulkneri L5             1401328  Bacteria   \n",
       "Candidatus Evansia muelleri                         1495769  Bacteria   \n",
       "Candidatus Gottesmanbacteria bacterium GW2011_G...  1618438  Bacteria   \n",
       "Candidatus Hodgkinia cicadicola                      573658  Bacteria   \n",
       "Candidatus Ishikawaella capsulata Mpkobe             476281  Bacteria   \n",
       "...                                                     ...       ...   \n",
       "Parcubacteria group bacterium GW2011_GWA1_60_11     1618805  Bacteria   \n",
       "Parcubacteria group bacterium GW2011_GWB1_45_7      1618878  Bacteria   \n",
       "Pelotomaculum thermopropionicum                      110500  Bacteria   \n",
       "Phytoplasma mali (strain AT)                         482235  Bacteria   \n",
       "Pseudomonas sp. 63_8                                1641374  Bacteria   \n",
       "Psychromonas sp. PRT-SC03                           1527299  Bacteria   \n",
       "Rhodobacteraceae bacterium HLUCCA09                 1666915  Bacteria   \n",
       "Rhodobacteraceae bacterium HLUCCA24                 1666918  Bacteria   \n",
       "Rickettsia prowazekii (strain Madrid E)              272947  Bacteria   \n",
       "Riesia pediculicola (strain USDA)                    515618  Bacteria   \n",
       "Ruthia magnifica subsp. Calyptogena magnifica        413404  Bacteria   \n",
       "SAR11 cluster bacterium PRT-SC02                    1527298  Bacteria   \n",
       "Saccharibacillus sacchari DSM 19268                  915437  Bacteria   \n",
       "Serratia symbiotica str. 'Cinara cedri'              568817  Bacteria   \n",
       "Sinorhizobium fredii GR64                            882101  Bacteria   \n",
       "Sulcia muelleri (strain GWSS)                        444179  Bacteria   \n",
       "Tropheryma whipplei (strain Twist) (Whipple's b...   203267  Bacteria   \n",
       "Uncultured termite group 1 bacterium phylotype ...   471821  Bacteria   \n",
       "Veillonella parvula                                   29466  Bacteria   \n",
       "Wigglesworthia glossinidia brevipalpis                36870  Bacteria   \n",
       "Wolbachia endosymbiont of Onchocerca ochengi         100901  Bacteria   \n",
       "Zinderia insecticola (strain CARI)                   871271  Bacteria   \n",
       "actinobacterium acAMD-2                             1504318  Bacteria   \n",
       "actinobacterium acIB-AMD-6                          1504321  Bacteria   \n",
       "actinobacterium acMicro-1                           1504316  Bacteria   \n",
       "candidate division WWE3 bacterium GW2011_GWA2_4...  1619110  Bacteria   \n",
       "candidate division WWE3 bacterium GW2011_GWA2_46_9  1619111  Bacteria   \n",
       "candidate division Zixibacteria bacterium DG_27     1703423  Bacteria   \n",
       "endosymbiont of Llaveia axin axin                   1415657  Bacteria   \n",
       "secondary endosymbiont of Heteropsylla cubana        134287  Bacteria   \n",
       "\n",
       "                                                    proteome_size  seq_cov  \\\n",
       "'Echinacea purpurea' witches'-broom phytoplasma               433       75   \n",
       "Actinobacteria bacterium BACL2 MAG-120920-bin34               999       88   \n",
       "Actinobacteria bacterium BACL4 MAG-120813-bin39               499       92   \n",
       "Amycolatopsis halophila YIM 93223                             356       79   \n",
       "Anaerolineae bacterium 49_20                                  966       83   \n",
       "Anaplasma marginale (strain Florida)                          938       80   \n",
       "Arsenophonus symbiont of Lipoptena fortisetosa                625      100   \n",
       "Atribacteria bacterium 34_128                                 834       89   \n",
       "Atribacteria bacterium 34_868                                 237       85   \n",
       "Azobacteroides pseudotrichonymphae genomovar. CFP2            847       86   \n",
       "Baumannia cicadellinicola subsp. Homalodisca co...            595       99   \n",
       "Bifidobacterium pseudocatenulatum                             986       86   \n",
       "Blattabacterium sp. (Cryptocercus punctulatus) ...            548       94   \n",
       "Blochmannia endosymbiont of Camponotus (Colobop...            584       99   \n",
       "Blochmannia endosymbiont of Polyrhachis (Hedomy...            589       99   \n",
       "Blochmannia floridanus                                        583      100   \n",
       "Borrelia turicatae (strain 91E135)                            818       82   \n",
       "Buchnera aphidicola (Cinara tujafilina)                       359       98   \n",
       "Buchnera aphidicola subsp. Acyrthosiphon pisum ...            572       98   \n",
       "Buchnera aphidicola subsp. Baizongia pistaciae ...            507       99   \n",
       "Buchnera aphidicola subsp. Cinara cedri (strain...            362       98   \n",
       "Buchnera aphidicola subsp. Schlechtendalia chin...            499       98   \n",
       "Candidatus Baumannia cicadellinicola                          550       96   \n",
       "Candidatus Carsonella ruddii DC                               206       75   \n",
       "Candidatus Curtissbacteria bacterium GW2011_GWA...            280       76   \n",
       "Candidatus Endolissoclinum faulkneri L5                       770       98   \n",
       "Candidatus Evansia muelleri                                   330       96   \n",
       "Candidatus Gottesmanbacteria bacterium GW2011_G...            336       75   \n",
       "Candidatus Hodgkinia cicadicola                               170       76   \n",
       "Candidatus Ishikawaella capsulata Mpkobe                      623       97   \n",
       "...                                                           ...      ...   \n",
       "Parcubacteria group bacterium GW2011_GWA1_60_11               237       76   \n",
       "Parcubacteria group bacterium GW2011_GWB1_45_7                359       75   \n",
       "Pelotomaculum thermopropionicum                               772       85   \n",
       "Phytoplasma mali (strain AT)                                  448       76   \n",
       "Pseudomonas sp. 63_8                                          605       80   \n",
       "Psychromonas sp. PRT-SC03                                     787       86   \n",
       "Rhodobacteraceae bacterium HLUCCA09                           634       85   \n",
       "Rhodobacteraceae bacterium HLUCCA24                           537       78   \n",
       "Rickettsia prowazekii (strain Madrid E)                       834       92   \n",
       "Riesia pediculicola (strain USDA)                             540       84   \n",
       "Ruthia magnifica subsp. Calyptogena magnifica                 976       93   \n",
       "SAR11 cluster bacterium PRT-SC02                              632       88   \n",
       "Saccharibacillus sacchari DSM 19268                           299       90   \n",
       "Serratia symbiotica str. 'Cinara cedri'                       672      100   \n",
       "Sinorhizobium fredii GR64                                     166       81   \n",
       "Sulcia muelleri (strain GWSS)                                 227       96   \n",
       "Tropheryma whipplei (strain Twist) (Whipple's b...            805       84   \n",
       "Uncultured termite group 1 bacterium phylotype ...            767       89   \n",
       "Veillonella parvula                                           923       83   \n",
       "Wigglesworthia glossinidia brevipalpis                        617       99   \n",
       "Wolbachia endosymbiont of Onchocerca ochengi                  647       89   \n",
       "Zinderia insecticola (strain CARI)                            206       95   \n",
       "actinobacterium acAMD-2                                       962       86   \n",
       "actinobacterium acIB-AMD-6                                    551       92   \n",
       "actinobacterium acMicro-1                                     873       86   \n",
       "candidate division WWE3 bacterium GW2011_GWA2_4...            365       76   \n",
       "candidate division WWE3 bacterium GW2011_GWA2_46_9            359       77   \n",
       "candidate division Zixibacteria bacterium DG_27               961       75   \n",
       "endosymbiont of Llaveia axin axin                             242       99   \n",
       "secondary endosymbiont of Heteropsylla cubana                 576       94   \n",
       "\n",
       "                                                    res_cov  \n",
       "'Echinacea purpurea' witches'-broom phytoplasma          58  \n",
       "Actinobacteria bacterium BACL2 MAG-120920-bin34          69  \n",
       "Actinobacteria bacterium BACL4 MAG-120813-bin39          73  \n",
       "Amycolatopsis halophila YIM 93223                        58  \n",
       "Anaerolineae bacterium 49_20                             62  \n",
       "Anaplasma marginale (strain Florida)                     55  \n",
       "Arsenophonus symbiont of Lipoptena fortisetosa           78  \n",
       "Atribacteria bacterium 34_128                            72  \n",
       "Atribacteria bacterium 34_868                            70  \n",
       "Azobacteroides pseudotrichonymphae genomovar. CFP2       68  \n",
       "Baumannia cicadellinicola subsp. Homalodisca co...       77  \n",
       "Bifidobacterium pseudocatenulatum                        62  \n",
       "Blattabacterium sp. (Cryptocercus punctulatus) ...       73  \n",
       "Blochmannia endosymbiont of Camponotus (Colobop...       78  \n",
       "Blochmannia endosymbiont of Polyrhachis (Hedomy...       78  \n",
       "Blochmannia floridanus                                   78  \n",
       "Borrelia turicatae (strain 91E135)                       58  \n",
       "Buchnera aphidicola (Cinara tujafilina)                  78  \n",
       "Buchnera aphidicola subsp. Acyrthosiphon pisum ...       79  \n",
       "Buchnera aphidicola subsp. Baizongia pistaciae ...       79  \n",
       "Buchnera aphidicola subsp. Cinara cedri (strain...       78  \n",
       "Buchnera aphidicola subsp. Schlechtendalia chin...       79  \n",
       "Candidatus Baumannia cicadellinicola                     77  \n",
       "Candidatus Carsonella ruddii DC                          67  \n",
       "Candidatus Curtissbacteria bacterium GW2011_GWA...       60  \n",
       "Candidatus Endolissoclinum faulkneri L5                  74  \n",
       "Candidatus Evansia muelleri                              77  \n",
       "Candidatus Gottesmanbacteria bacterium GW2011_G...       63  \n",
       "Candidatus Hodgkinia cicadicola                          62  \n",
       "Candidatus Ishikawaella capsulata Mpkobe                 79  \n",
       "...                                                     ...  \n",
       "Parcubacteria group bacterium GW2011_GWA1_60_11          64  \n",
       "Parcubacteria group bacterium GW2011_GWB1_45_7           62  \n",
       "Pelotomaculum thermopropionicum                          69  \n",
       "Phytoplasma mali (strain AT)                             60  \n",
       "Pseudomonas sp. 63_8                                     65  \n",
       "Psychromonas sp. PRT-SC03                                67  \n",
       "Rhodobacteraceae bacterium HLUCCA09                      64  \n",
       "Rhodobacteraceae bacterium HLUCCA24                      65  \n",
       "Rickettsia prowazekii (strain Madrid E)                  67  \n",
       "Riesia pediculicola (strain USDA)                        77  \n",
       "Ruthia magnifica subsp. Calyptogena magnifica            75  \n",
       "SAR11 cluster bacterium PRT-SC02                         72  \n",
       "Saccharibacillus sacchari DSM 19268                      67  \n",
       "Serratia symbiotica str. 'Cinara cedri'                  77  \n",
       "Sinorhizobium fredii GR64                                61  \n",
       "Sulcia muelleri (strain GWSS)                            77  \n",
       "Tropheryma whipplei (strain Twist) (Whipple's b...       64  \n",
       "Uncultured termite group 1 bacterium phylotype ...       71  \n",
       "Veillonella parvula                                      64  \n",
       "Wigglesworthia glossinidia brevipalpis                   76  \n",
       "Wolbachia endosymbiont of Onchocerca ochengi             69  \n",
       "Zinderia insecticola (strain CARI)                       76  \n",
       "actinobacterium acAMD-2                                  64  \n",
       "actinobacterium acIB-AMD-6                               73  \n",
       "actinobacterium acMicro-1                                66  \n",
       "candidate division WWE3 bacterium GW2011_GWA2_4...       53  \n",
       "candidate division WWE3 bacterium GW2011_GWA2_46_9       55  \n",
       "candidate division Zixibacteria bacterium DG_27          57  \n",
       "endosymbiont of Llaveia axin axin                        77  \n",
       "secondary endosymbiont of Heteropsylla cubana            77  \n",
       "\n",
       "[106 rows x 5 columns]"
      ]
     },
     "execution_count": 164,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "b[ b[ 'proteome_size']< 1000 ]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 150,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(array([  2.,   6.,   6.,  25.,  15.,  22.,  19.,   9.,   9.,   5.,   2.,\n",
       "          8.,  15.]),\n",
       " array([66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79]),\n",
       " <a list of 13 Patch objects>)"
      ]
     },
     "execution_count": 150,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAAXQAAAD8CAYAAABn919SAAAABHNCSVQICAgIfAhkiAAAAAlwSFlz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\nOwAAAABJRU5ErkJggg==\n",
      "text/plain": [
       "<matplotlib.figure.Figure at 0x7fcd5e9c1400>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "hist(b['res_cov'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 202,
   "metadata": {},
   "outputs": [],
   "source": [
    "large_proteome = data['proteome_size']>1000\n",
    "\n",
    "accessions = data[isBacteria & covered & large_proteome]['pfam_id']\n",
    "tmp = accessions.to_dict()\n",
    "nums = {tmp[key]:key for key in tmp}\n",
    "nums\n",
    "import pickle\n",
    "f=open('list.pkl', 'wb')\n",
    "pickle.dump(nums, f)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.6.0"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}