biotools-biocontainers-venn.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# overlap study for bioconda and biotools"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## get list of biotools entries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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    },
    {
     "name": "stdout",
     "output_type": "stream",
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      "getting page ?page=610\n",
      "getting page ?page=611\n",
      "getting page ?page=612\n",
      "getting page ?page=613\n",
      "getting page ?page=614\n",
      "getting page ?page=615\n",
      "getting page ?page=616\n",
      "getting page ?page=617\n",
      "getting page ?page=618\n",
      "getting page ?page=619\n",
      "getting page ?page=620\n",
      "getting page ?page=621\n",
      "getting page ?page=622\n",
      "getting page ?page=623\n",
      "getting page ?page=624\n"
     ]
    }
   ],
   "source": [
    "import requests\n",
    "biotools_list = []\n",
    "next_biotools_page = '?page=1'\n",
    "while next_biotools_page is not None:\n",
    "    print('getting page %s' % next_biotools_page)\n",
    "    page = requests.get('https://bio.tools/api/tool/' + next_biotools_page).json()\n",
    "    biotools_list += page['list']\n",
    "    next_biotools_page = page['next']"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "_and get the list of biotools ids for these entries_"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pandas import DataFrame\n",
    "biotools_ids = [element['id'] for element in biotools_list]\n",
    "biotools_ids_processed = {}\n",
    "for b in biotools_list:\n",
    "    if 'BioConductor' in b['collectionID']:\n",
    "        biotools_ids_processed['BIOCONDUCTOR-%s' % b['id'].upper()] = b['id']\n",
    "    if 'EMBOSS' in b['collectionID']:\n",
    "        biotools_ids_processed['BIOCONDUCTOR-%s' % b['id'].upper()] = b['id']\n",
    "    else:\n",
    "        biotools_ids_processed[b['id'].upper()] = b['id']\n",
    "biotools_ids = DataFrame(list(biotools_ids_processed.items()), columns=['common', 'biotools'])\n",
    "biotools_ids = biotools_ids.set_index('common')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## get list of bioconda entries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2017-10-10 12:20:14--  https://conda.anaconda.org/bioconda/linux-64/repodata.json\n",
      "Resolving conda.anaconda.org (conda.anaconda.org)... 104.16.193.233, 104.16.192.233\n",
      "Connecting to conda.anaconda.org (conda.anaconda.org)|104.16.193.233|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: unspecified [application/json]\n",
      "Saving to: ‘repodata.json’\n",
      "\n",
      "repodata.json           [<=>                 ]   5,38M  1,23MB/s    in 8,2s    \n",
      "\n",
      "2017-10-10 12:20:23 (669 KB/s) - ‘repodata.json’ saved [5642605]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "#repodata_url = 'https://conda.anaconda.org/bioconda/linux-64/repodata.json'\n",
    "#repodata = requests.get(repodata_url).json()\n",
    "!rm repodata.json && wget https://conda.anaconda.org/bioconda/linux-64/repodata.json\n",
    "import json\n",
    "bioconda_list = json.load(open('repodata.json'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "10261\n"
     ]
    }
   ],
   "source": [
    "print(len(bioconda_list['packages'].items()))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "_and get the list of bioconda package names_"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                                                biotools\n",
      "common                                                  \n",
      "BINDN                                              bindn\n",
      "CLEANTRANSCRIPTFILE-IP            cleantranscriptfile-ip\n",
      "DENDRIX                                          dendrix\n",
      "REFPLUS                                          refplus\n",
      "ALGGEN                                            alggen\n",
      "IELM                                                ielm\n",
      "PROTEOME-PI                                  proteome-pi\n",
      "CROPPAL                                          croppal\n",
      "OGSA                                                ogsa\n",
      "KEGG                                                kegg\n",
      "FASTA                                              fasta\n",
      "SEQUENCESERVER                            SequenceServer\n",
      "HGV_LINKTOGPROFILE-IP              hgv_linktogprofile-ip\n",
      "BIOCONDUCTOR-RDISOP                               rdisop\n",
      "GMRP                                                gmrp\n",
      "BIOCONDUCTOR-SUPRAHEX                           suprahex\n",
      "JTRAML                                            jtraml\n",
      "GENERECOMMENDER                          generecommender\n",
      "NETGENE2                                        netgene2\n",
      "BIOCONDUCTOR-BANANA                               banana\n",
      "HARMAN                                            harman\n",
      "PHMMER                                            phmmer\n",
      "IREFR                                              irefr\n",
      "TITANCNA                                        titancna\n",
      "JRONN_WS_JABAWS                          jronn_ws_jabaws\n",
      "MASSTRIX                                        masstrix\n",
      "POLYBAYES                                      PolyBayes\n",
      "PREDHS                                            PredHS\n",
      "CHC_FIND                                        chc_find\n",
      "BIOCONDUCTOR-UNIPROT.WS                       uniprot.ws\n",
      "...                                                  ...\n",
      "MAPDAMAGE                                      mapdamage\n",
      "MULTIBIND                                      multibind\n",
      "SWISS-PROT                                    swiss-prot\n",
      "HMDB                                                hmdb\n",
      "MOLECULAR_WEIGHT_CALCULATOR  molecular_weight_calculator\n",
      "BIOCONDUCTOR-DAN                                     dan\n",
      "PATTERNLAB                                    patternlab\n",
      "BACELLO                                          bacello\n",
      "MAKER                                              maker\n",
      "ROC                                                  roc\n",
      "TATP                                                tatp\n",
      "IDCONVERT                                      idconvert\n",
      "BIOCONDUCTOR-PROLOCGUI                         prolocgui\n",
      "MCPROMOTER                                    McPromoter\n",
      "COMPSS                                            compss\n",
      "INGAP-SV                                        ingap-sv\n",
      "MBASED                                            mbased\n",
      "SEQMINER                                        seqminer\n",
      "COMBREX                                          combrex\n",
      "PRORATA                                          prorata\n",
      "CHIPXPRESS                                    chipxpress\n",
      "RAPIDO                                            rapido\n",
      "BIOCONDUCTOR-BACKTRANSEQ                     backtranseq\n",
      "INT_HAPMAP_PROJECT                    Int_HapMap_Project\n",
      "PICARD_FASTQTOSAM-IP                picard_fastqtosam-ip\n",
      "COXPRESDB                                      coxpresdb\n",
      "TASR                                                tasr\n",
      "DRCANCER                                        drcancer\n",
      "ALPHAPRED                                      AlphaPred\n",
      "SWEED                                              SweeD\n",
      "\n",
      "[7217 rows x 1 columns]\n",
      "                                                                            bioconda\n",
      "common                                                                              \n",
      "PYQUERY                                                                      pyquery\n",
      "LIKENESS                                                          np-likeness-scorer\n",
      "LIBIDN                                                                        libidn\n",
      "WEEDER                                                                        weeder\n",
      "POMEGRANATE                                                              pomegranate\n",
      "AUTODTD                                                                 ucsc-autodtd\n",
      "BIOCONDUCTOR-MOTIFRG                                            bioconductor-motifrg\n",
      "MUSCLE                                                                        muscle\n",
      "BWAKIT                                                                        bwakit\n",
      "KID                                                                              kid\n",
      "SEQ                                                                          bpp-seq\n",
      "GENONETS                                                                    genonets\n",
      "DAISYSUITE                                                                daisysuite\n",
      "WS4PY                                                                          ws4py\n",
      "ORTHOMCL                                                                    orthomcl\n",
      "DSK                                                                              dsk\n",
      "PSLPOSTARGET                                                       ucsc-pslpostarget\n",
      "BIOCONDUCTOR-BIONET                                              bioconductor-bionet\n",
      "BIOCONDUCTOR-METHYLKIT                                        bioconductor-methylkit\n",
      "BIOCONDUCTOR-TITANCNA                                          bioconductor-titancna\n",
      "BIOCONDUCTOR-ROC                                                    bioconductor-roc\n",
      "TRIMCLUSTER                                                            r-trimcluster\n",
      "BIOCONDUCTOR-PODKAT                                              bioconductor-podkat\n",
      "BIOCONDUCTOR-CELLNOPTR                                        bioconductor-cellnoptr\n",
      "PULLSEQ                                                                      pullseq\n",
      "MAFMEFIRST                                                           ucsc-mafmefirst\n",
      "IGV                                                                              igv\n",
      "FANN                                                                            fann\n",
      "FICUS                                                                          ficus\n",
      "COLORMAP                                                                    colormap\n",
      "...                                                                              ...\n",
      "REGIONS                                                                 gvcf-regions\n",
      "SUBCHAR                                                                 ucsc-subchar\n",
      "AUTHEN                                                     perl-authen-sasl-saslprep\n",
      "VERSE                                                                          verse\n",
      "BIOCONDUCTOR-JMOSAICS                                          bioconductor-jmosaics\n",
      "IMAGE                                                                perl-image-info\n",
      "GDSCTOOLS                                                                  gdsctools\n",
      "PARAVIEW                                                                    paraview\n",
      "SVVIZ                                                                          svviz\n",
      "NUCLEOATAC                                                                nucleoatac\n",
      "BH                                                                              r-bh\n",
      "BIOCONDUCTOR-FDB.INFINIUMMETHYLATION.HG19  bioconductor-fdb.infiniummethylation.hg19\n",
      "TALLOC                                                                        talloc\n",
      "JSON_COLLECT_DATA_SOURCE                                    json_collect_data_source\n",
      "SWARM                                                                          swarm\n",
      "DUNOVO                                                                        dunovo\n",
      "ESTSCAN2                                                               perl-estscan2\n",
      "RNASEQ                                                                  bcbio-rnaseq\n",
      "TOOLS                                                                transrate-tools\n",
      "BIOCONDUCTOR-RECOUP                                              bioconductor-recoup\n",
      "BIOCONDUCTOR-GENOMEINFODBDATA                          bioconductor-genomeinfodbdata\n",
      "LIBXML                                                              perl-libxml-perl\n",
      "BIOCONDUCTOR-OLIGO                                                bioconductor-oligo\n",
      "GETRNA                                                                   ucsc-getrna\n",
      "ETA                                                                              eta\n",
      "GADEM                                                                          gadem\n",
      "BAMHASH                                                                      bamhash\n",
      "INTARNA                                                                      intarna\n",
      "POTION                                                                  flask-potion\n",
      "RNASTRUCTURE                                                            rnastructure\n",
      "\n",
      "[2567 rows x 1 columns]\n"
     ]
    }
   ],
   "source": [
    "#bioconda_ids = [element['name'] for element in bioconda_list]\n",
    "#print(bioconda_ids))\n",
    "bioconda_ids = set([package['name'] for key, package in bioconda_list['packages'].items()])\n",
    "bioconda_ids_processed = {}\n",
    "for bioconda_id in bioconda_ids:\n",
    "    if len(bioconda_id.split('-'))>1 and bioconda_id.split('-')[0]!='bioconductor':\n",
    "        bioconda_ids_processed[bioconda_id.split('-')[1].upper()] = bioconda_id\n",
    "    else:\n",
    "        bioconda_ids_processed[bioconda_id.upper()] = bioconda_id\n",
    "bioconda_ids = DataFrame(list(bioconda_ids_processed.items()), columns=['common', 'bioconda'])\n",
    "bioconda_ids = bioconda_ids.set_index('common')\n",
    "print(biotools_ids)\n",
    "print(bioconda_ids)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "this is the intersection of biotools/biocondas entries, based on strict name equality"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [],
   "source": [
    "bioconda_ids.join(biotools_ids).to_csv('mapping.csv',na_rep='null')\n",
    "bioconda_ids.join(biotools_ids).dropna().to_csv('mapping_matchonly.csv',na_rep='null')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[]\n"
     ]
    }
   ],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 122,
   "metadata": {},
   "outputs": [],
   "source": [
    "not_in_bioconda =  set([b.upper() for b in biotools_ids]) - set([b.upper() for b in bioconda_ids])\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 125,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "set()\n"
     ]
    }
   ],
   "source": [
    "not_in_biotools = set([b.upper() for b in bioconda_ids]) - set([b.upper() for b in biotools_ids])\n",
    "print(not_in_biotools)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 111,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<matplotlib_venn._common.VennDiagram at 0x7f22a861deb8>"
      ]
     },
     "execution_count": 111,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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      "text/plain": [
       "<matplotlib.figure.Figure at 0x7f22a87156d8>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib inline\n",
    "from matplotlib_venn import venn2\n",
    "venn2(subsets=(len(biotools_ids), len(bioconda_ids), intersection), set_labels = ('bio.tools', 'bioconda', 'overlap'))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "questions:\n",
    "* non-bioinformatics conda packages (yamllint?)\n",
    "* packages that include a version number in biotools: ggplot2\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[{'arch': 'x86_64',\n",
       "  'binstar': {'channel': 'main',\n",
       "   'owner_id': '55f35cc885a76554d7c66613',\n",
       "   'package_id': '562657e9d6f51f0b163323ba'},\n",
       "  'build': '0',\n",
       "  'build_number': 0,\n",
       "  'depends': ['bioconductor-annotationdbi >=1.27.9',\n",
       "   'bioconductor-biobase',\n",
       "   'bioconductor-biocgenerics >=0.15.3',\n",
       "   'bioconductor-biostrings >=2.33.5',\n",
       "   'bioconductor-bsgenome >=1.37.6',\n",
       "   'bioconductor-genomeinfodb >=1.1.3',\n",
       "   'bioconductor-genomicfeatures >=1.19.17',\n",
       "   'bioconductor-genomicranges >=1.19.47',\n",
       "   'bioconductor-iranges >=2.3.25',\n",
       "   'bioconductor-rsamtools >=1.19.52',\n",
       "   'bioconductor-rtracklayer >=1.25.16',\n",
       "   'bioconductor-s4vectors >=0.7.11',\n",
       "   'bioconductor-summarizedexperiment >=0.3.1',\n",
       "   'bioconductor-xvector >=0.5.6',\n",
       "   'bioconductor-zlibbioc',\n",
       "   'r >=2.8.0',\n",
       "   'r-dbi'],\n",
       "  'license': 'Artistic-2.0',\n",
       "  'machine': 'x86_64',\n",
       "  'md5': '7e2c7475f6d59cdddbb995aa969b57f3',\n",
       "  'name': 'bioconductor-variantannotation',\n",
       "  'operatingsystem': 'linux',\n",
       "  'platform': 'linux',\n",
       "  'requires': [],\n",
       "  'size': 1980788,\n",
       "  'subdir': 'linux-64',\n",
       "  'target-triplet': 'x86_64-any-linux',\n",
       "  'version': '1.16.1'},\n",
       " {'arch': 'x86_64',\n",
       "  'binstar': {'channel': 'main',\n",
       "   'owner_id': '55f35cc885a76554d7c66613',\n",
       "   'package_id': '562657e9d6f51f0b163323ba'},\n",
       "  'build': 'r3.3.1_0',\n",
       "  'build_number': 0,\n",
       "  'depends': ['bioconductor-annotationdbi >=1.27.9',\n",
       "   'bioconductor-biobase',\n",
       "   'bioconductor-biocgenerics >=0.15.3',\n",
       "   'bioconductor-biostrings >=2.33.5',\n",
       "   'bioconductor-bsgenome >=1.37.6',\n",
       "   'bioconductor-genomeinfodb >=1.7.1',\n",
       "   'bioconductor-genomicfeatures >=1.19.17',\n",
       "   'bioconductor-genomicranges >=1.19.47',\n",
       "   'bioconductor-iranges >=2.3.25',\n",
       "   'bioconductor-rsamtools >=1.23.10',\n",
       "   'bioconductor-rtracklayer >=1.25.16',\n",
       "   'bioconductor-s4vectors >=0.9.47',\n",
       "   'bioconductor-summarizedexperiment >=0.3.1',\n",
       "   'bioconductor-xvector >=0.5.6',\n",
       "   'bioconductor-zlibbioc',\n",
       "   'r 3.3.1*',\n",
       "   'r-dbi'],\n",
       "  'has_prefix': False,\n",
       "  'license': 'Artistic-2.0',\n",
       "  'machine': 'x86_64',\n",
       "  'md5': 'c43c37e78cc910a8e8f04a1f792fcb08',\n",
       "  'name': 'bioconductor-variantannotation',\n",
       "  'operatingsystem': 'linux',\n",
       "  'platform': 'linux',\n",
       "  'requires': [],\n",
       "  'size': 2386659,\n",
       "  'subdir': 'linux-64',\n",
       "  'target-triplet': 'x86_64-any-linux',\n",
       "  'version': '1.20.3'},\n",
       " {'arch': 'x86_64',\n",
       "  'binstar': {'channel': 'main',\n",
       "   'owner_id': '55f35cc885a76554d7c66613',\n",
       "   'package_id': '562657e9d6f51f0b163323ba'},\n",
       "  'build': '0',\n",
       "  'build_number': 0,\n",
       "  'depends': ['bioconductor-annotationdbi >=1.27.9',\n",
       "   'bioconductor-biobase',\n",
       "   'bioconductor-biocgenerics >=0.15.3',\n",
       "   'bioconductor-biostrings >=2.33.5',\n",
       "   'bioconductor-bsgenome >=1.37.6',\n",
       "   'bioconductor-genomeinfodb >=1.1.3',\n",
       "   'bioconductor-genomicfeatures >=1.19.17',\n",
       "   'bioconductor-genomicranges >=1.19.47',\n",
       "   'bioconductor-iranges >=2.3.25',\n",
       "   'bioconductor-rsamtools >=1.19.52',\n",
       "   'bioconductor-rtracklayer >=1.25.16',\n",
       "   'bioconductor-s4vectors >=0.7.11',\n",
       "   'bioconductor-summarizedexperiment >=0.3.1',\n",
       "   'bioconductor-xvector >=0.5.6',\n",
       "   'bioconductor-zlibbioc',\n",
       "   'r >=2.8.0',\n",
       "   'r-dbi'],\n",
       "  'license': 'Artistic-2.0',\n",
       "  'machine': 'x86_64',\n",
       "  'md5': 'aae18d3c7c4e358d380ca3390f75680e',\n",
       "  'name': 'bioconductor-variantannotation',\n",
       "  'operatingsystem': 'linux',\n",
       "  'platform': 'linux',\n",
       "  'requires': [],\n",
       "  'size': 1982400,\n",
       "  'subdir': 'linux-64',\n",
       "  'target-triplet': 'x86_64-any-linux',\n",
       "  'version': '1.16.4'},\n",
       " {'arch': 'x86_64',\n",
       "  'binstar': {'channel': 'main',\n",
       "   'owner_id': '55f35cc885a76554d7c66613',\n",
       "   'package_id': '562657e9d6f51f0b163323ba'},\n",
       "  'build': 'r3.3.2_0',\n",
       "  'build_number': 0,\n",
       "  'depends': ['bioconductor-annotationdbi >=1.27.9',\n",
       "   'bioconductor-biobase',\n",
       "   'bioconductor-biocgenerics >=0.15.3',\n",
       "   'bioconductor-biostrings >=2.33.5',\n",
       "   'bioconductor-bsgenome >=1.37.6',\n",
       "   'bioconductor-genomeinfodb >=1.7.1',\n",
       "   'bioconductor-genomicfeatures >=1.19.17',\n",
       "   'bioconductor-genomicranges >=1.19.47',\n",
       "   'bioconductor-iranges >=2.3.25',\n",
       "   'bioconductor-rsamtools >=1.23.10',\n",
       "   'bioconductor-rtracklayer >=1.25.16',\n",
       "   'bioconductor-s4vectors >=0.9.47',\n",
       "   'bioconductor-summarizedexperiment >=0.3.1',\n",
       "   'bioconductor-xvector >=0.5.6',\n",
       "   'bioconductor-zlibbioc',\n",
       "   'r-base 3.3.2*',\n",
       "   'r-dbi'],\n",
       "  'has_prefix': False,\n",
       "  'license': 'Artistic-2.0',\n",
       "  'machine': 'x86_64',\n",
       "  'md5': '57b392256753a0d525e9167453e7ab22',\n",
       "  'name': 'bioconductor-variantannotation',\n",
       "  'operatingsystem': 'linux',\n",
       "  'platform': 'linux',\n",
       "  'requires': [],\n",
       "  'size': 2387193,\n",
       "  'subdir': 'linux-64',\n",
       "  'target-triplet': 'x86_64-any-linux',\n",
       "  'version': '1.20.3'},\n",
       " {'arch': 'x86_64',\n",
       "  'binstar': {'channel': 'main',\n",
       "   'owner_id': '55f35cc885a76554d7c66613',\n",
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       "   'bioconductor-zlibbioc',\n",
       "   'r-base 3.4.1*',\n",
       "   'r-dbi'],\n",
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       "   'bioconductor-bsgenome >=1.37.6',\n",
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       "   'bioconductor-zlibbioc',\n",
       "   'r >=2.8.0',\n",
       "   'r-dbi'],\n",
       "  'license': 'Artistic-2.0',\n",
       "  'machine': 'x86_64',\n",
       "  'md5': 'f9182e4d677a705b0cc11125f572e9ad',\n",
       "  'name': 'bioconductor-variantannotation',\n",
       "  'operatingsystem': 'linux',\n",
       "  'platform': 'linux',\n",
       "  'requires': [],\n",
       "  'size': 1983074,\n",
       "  'subdir': 'linux-64',\n",
       "  'target-triplet': 'x86_64-any-linux',\n",
       "  'version': '1.16.3'}]"
      ]
     },
     "execution_count": 68,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[package for key, package in bioconda_list['packages'].items() if package['name']=='bioconductor-variantannotation']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "253"
      ]
     },
     "execution_count": 75,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len([element for element in biotools_list if 'EMBOSS' in element['collectionID']])"
   ]
  }
 ],
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