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    "info": {
        "author": "Vera Alvarez, Roberto",
        "author_email": "veraalva@ncbi.nlm.nih.gov",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Framework :: Jupyter",
            "Intended Audience :: Science/Research",
            "License :: Public Domain",
            "Natural Language :: English",
            "Operating System :: Unix",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "GO Enrichment package\n---------------------\n\nThis package execute GO enrichment analysis froma list of gene names using a precomputed database.\nThe GO terms are analyze using a hypergeometric test.\n\nGO enrichment database\n----------------------\n\nThe GO graph structure is created from the Gene Ontology OBO \nfile http://current.geneontology.org/ontology/go.obo\n\nNCBI gene\n---------\n\nThe NCBI gene database is used to include genes to the GO terms graph. The required files are:\nftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz and\nftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz\n\nThese files can be filter for a specific taxonomy id. This example is for human: 9606\n\n    gunzip -c gene_info.gz | grep -P \"^9606\\t\" > gene_info_${taxid}\n    gzip gene_info_${taxid}\n    gunzip -c gene2go.gz | grep -P \"^9606\\t\" > gene2go_${taxid}\n    gzip gene2go_${taxid}\n\n\nUniprot GOA\n-----------\n\nThe Uniprot GOA files can be also used to add more genes to the GO graph.\nThe complete file is: \nftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz\n\nUniprot GOA also include some pre-filtered organism: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/\n\nTSV file: gene\\<tab\\>GO term\n----------------------------\n\nAny TSV file with the relationship between gene names and GO term can also be included into the database.\nThe file just need to include in the first column the gene name and in the second column the GO term. \nAny other extra column will be ignored. \n\nEnsembl BioMart\n---------------\n\nThe Ensembl data can be alos include using their BioMart tool. Go to the Ensembl Biomart website: \nhttp://useast.ensembl.org/biomart/.\nUsing this tool a TSV file can be generated with\ngene names in the first column and GO term in the second column.\n\nDatabase creation\n-----------------\n\nThis example is for human. Please, note all input files should be gzipped.\n\n    python ./bin/goenrichDB.py --gene_info gene_info.gz --gene2go gene2go.gz --goa_uniprot goa_uniprot_all.gaf.gz --gobo go.obo --taxid 9606 --goenrichDB goenrichDB_20190419.pickle\n\n\nUsage\n-----\n\n\n    usage: goenrichDB.py [-h] [--gene_info GENE_INFO] [--gene2go GENE2GO]\n                         [--tsv TSV] [--goenrichDB GOENRICHDB]\n                         [--goa_uniprot GOA_UNIPROT] [--gobo GOBO] [--taxid TAXID]\n                         -o O\n\n    Creates pickle data structure used by \"goenrich.py\"\n\n    optional arguments:\n        -h, --help            show this help message and exit\n        --gene_info GENE_INFO\n                            NCBI gene_info file\n        --gene2go GENE2GO     NCBI gene2go file\n        --tsv TSV             TSV file with at least two columns: Gene_name<tab>GO\n                            terms\n        --goenrichDB GOENRICHDB\n                            Previous created goenrich pickle file. The new genes\n                            will be added to this database\n        --goa_uniprot GOA_UNIPROT\n                            Uniprot GOA file GAF format\n        --gobo GOBO           UGO Obo file from Gene Ontology\n        --taxid TAXID         Process genes for tax id if it is possible\n        -o O                  Pickle output file name\n\n\nPre-computed databases\n----------------------\n\nWe offer some pre-computed database https://ftp.ncbi.nlm.nih.gov/pub/goenrichment/\n\nGo enrichment analysis\n----------------------\n\nThe analysis is executed using the script `goenrich.py`. The input file is a text file with \none gene name per line.\n\n\n    ./bin/goenrich.py --goenrichDB gene2GO_human.pickle -i query.tsv -o goenrich.tsv\n\n\nThe `gene2GO_human.pickle` can be downloaded from https://ftp.ncbi.nlm.nih.gov/pub/goenrichment/goenrichDB_human.pickle\n\n    usage: goenrich.py [-h] -i I -o O [--goenrichDB GOENRICHDB]\n                       [--min_category_depth MIN_CATEGORY_DEPTH]\n                       [--min_category_size MIN_CATEGORY_SIZE]\n                       [--max_category_size MAX_CATEGORY_SIZE] [--alpha ALPHA]\n\n    Calculate GO enrichment from a list of genes. Default database organism: human\n\n    optional arguments:\n        -h, --help            show this help message and exit\n        -i I                  Input list of gene names\n        -o O                  TSV file with all results\n        --goenrichDB GOENRICHDB\n                            Gene2GO pickle file created with \"goenrichDB.py\". If\n                            not provided the database is loaded from:\n        --min_category_depth MIN_CATEGORY_DEPTH\n                            Min GO term graph depth to include in the report.\n                            Default: 4\n        --min_category_size MIN_CATEGORY_SIZE\n                            Min number of gene in a GO term to include in the\n                            report. Default: 3\n        --max_category_size MAX_CATEGORY_SIZE\n                            Max number of gene in a GO term to include in the\n                            report. Default: 500\n        --alpha ALPHA         Alpha value for p-value correction. Default: 0.05\n\n\nRequirements\n------------\n\n * Python 3.7\n     * numpy\n     * scipy\n     * statsmodels\n     * pandas\n     * networkx\n\n\nPublic Domain notice\n--------------------\n\nNational Center for Biotechnology Information.\n\nThis software is a \"United States Government Work\" under the terms of the United States\nCopyright Act. It was written as part of the authors' official duties as United States\nGovernment employees and thus cannot be copyrighted. This software is freely available\nto the public for use. The National Library of Medicine and the U.S. Government have not\n placed any restriction on its use or reproduction.\n\nAlthough all reasonable efforts have been taken to ensure the accuracy and reliability\nof the software and data, the NLM and the U.S. Government do not and cannot warrant the\nperformance or results that may be obtained by using this software or data. The NLM and\nthe U.S. Government disclaim all warranties, express or implied, including warranties\nof performance, merchantability or fitness for any particular purpose.\n\nPlease cite NCBI in any work or product based on this material.\n\n\n",
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