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"author": "Jan Daniel Rudolph",
"author_email": "jan.daniel.rudolph@gmail.com",
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"classifiers": [
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 2.7",
"Programming Language :: Python :: 3.4",
"Topic :: Scientific/Engineering :: Bio-Informatics",
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"description": "goenrich\n========\n\n.. image:: https://badges.gitter.im/Join%20Chat.svg\n :target: https://gitter.im/jdrudolph/goenrich?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge\n\n.. image:: https://readthedocs.org/projects/goenrich/badge/?version=latest\n :target: https://goenrich.readthedocs.org/en/latest\n\n.. image:: https://travis-ci.org/jdrudolph/goenrich.svg?branch=master\n :target: https://travis-ci.org/jdrudolph/goenrich\n\nConvenient GO enrichments from python. For use in ``python`` projects.\n\n#. Builds the GO-ontology graph\n#. Propagates GO-annotations up the graph\n#. Performs enrichment test for all categories\n#. Performs multiple testing correction\n#. Allows for export to ``pandas`` for processing and ``graphviz`` for\n visualization\n\nInstallation\n------------\n\n| Install package from pypi and download ontology and needed annotations.\n\n.. code:: shell\n\n pip install goenrich\n mkdir db\n # Ontology\n wget http://purl.obolibrary.org/obo/go/go-basic.obo -O db/go-basic.obo\n # UniprotACC\n wget http://geneontology.org/gene-associations/goa_human.gaf.gz -O db/gene_association.goa_human.gaf.gz\n # Yeast SGD\n wget http://downloads.yeastgenome.org/curation/literature/gene_association.sgd.gz -O db/gene_association.sgd.gz\n # Entrez GeneID\n wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz -O db/gene2go.gz\n\nRun GO enrichment\n-----------------\n\n.. code:: python\n\n import goenrich\n\n # build the ontology\n O = goenrich.obo.ontology('db/go-basic.obo')\n\n # use all entrez geneid associations form gene2go as background\n # use annot = goenrich.read.goa('db/gene_association.goa_human.gaf.gz') for uniprot\n # use annot = goenrich.read.sgd('db/gene_association.sgd.gz') for yeast\n gene2go = goenrich.read.gene2go('db/gene2go.gz')\n # use values = {k: set(v) for k,v in annot.groupby('go_id')['db_object_symbol']} for uniprot/yeast\n values = {k: set(v) for k,v in gene2go.groupby('GO_ID')['GeneID']}\n\n # propagate the background through the ontology\n background_attribute = 'gene2go'\n goenrich.enrich.propagate(O, values, background_attribute)\n\n # extract some list of entries as example query\n # use query = annot['db_object_symbol'].unique()[:20]\n query = gene2go['GeneID'].unique()[:20]\n\n # for additional export to graphviz just specify the gvfile argument\n # the show argument keeps the graph reasonably small\n df = goenrich.enrich.analyze(O, query, background_attribute, gvfile='test.dot')\n\n # generate html\n df.dropna().head().to_html('example.html')\n\n # call to graphviz\n import subprocess\n subprocess.check_call(['dot', '-Tpng', 'test.dot', '-o', 'test.png'])\n\nGenerate ``png`` image using graphviz:\n\n.. code:: shell\n\n dot -Tpng example.dot > example.png\n\nor directly from python:\n\n.. code:: python\n\n import subprocess\n subprocess.check_call(['dot', '-Tpng', 'example.dot', '-o', 'example.png'])\n\n.. image:: https://cloud.githubusercontent.com/assets/2606663/8525018/cad3a288-23fe-11e5-813c-bd205a47eed8.png\n\nCheck the documentation for all available parameters\n\nLicence & Contributors\n======================\n\nThis work is licenced under the MIT licence\n\nContributions are welcome!\n\nSpecial thanks\n--------------\n\n- `@lukauskas `_ for implementing i/o support for file-like objects.\n- `@zfrenchee `_ for fixing a bug in the calculation of the test statistic.\n- `@pommy1 `_ for implementing support for `networkx >= 2.0.0`.\n\nBuilding the documentation\n==========================\n\n.. code:: shell\n\n sphinx-apidoc -f -o docs goenrich goenrich/tests",
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