goenrich
Convenient GO enrichments from python. For use in python projects.
Builds the GO-ontology graph
Propagates GO-annotations up the graph
Performs enrichment test for all categories
Performs multiple testing correction
Allows for export to pandas for processing and graphviz for visualization
Installation
pip install goenrich
mkdir db
# Ontology
wget http://purl.obolibrary.org/obo/go/go-basic.obo -O db/go-basic.obo
# UniprotACC
wget http://geneontology.org/gene-associations/goa_human.gaf.gz -O db/gene_association.goa_human.gaf.gz
# Yeast SGD
wget http://downloads.yeastgenome.org/curation/literature/gene_association.sgd.gz -O db/gene_association.sgd.gz
# Entrez GeneID
wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz -O db/gene2go.gzRun GO enrichment
import goenrich
# build the ontology
O = goenrich.obo.ontology('db/go-basic.obo')
# use all entrez geneid associations form gene2go as background
# use annot = goenrich.read.goa('db/gene_association.goa_human.gaf.gz') for uniprot
# use annot = goenrich.read.sgd('db/gene_association.sgd.gz') for yeast
gene2go = goenrich.read.gene2go('db/gene2go.gz')
# use values = {k: set(v) for k,v in annot.groupby('go_id')['db_object_symbol']} for uniprot/yeast
values = {k: set(v) for k,v in gene2go.groupby('GO_ID')['GeneID']}
# propagate the background through the ontology
background_attribute = 'gene2go'
goenrich.enrich.propagate(O, values, background_attribute)
# extract some list of entries as example query
# use query = annot['db_object_symbol'].unique()[:20]
query = gene2go['GeneID'].unique()[:20]
# for additional export to graphviz just specify the gvfile argument
# the show argument keeps the graph reasonably small
df = goenrich.enrich.analyze(O, query, background_attribute, gvfile='test.dot')
# generate html
df.dropna().head().to_html('example.html')
# call to graphviz
import subprocess
subprocess.check_call(['dot', '-Tpng', 'test.dot', '-o', 'test.png'])Generate png image using graphviz:
dot -Tpng example.dot > example.pngor directly from python:
import subprocess
subprocess.check_call(['dot', '-Tpng', 'example.dot', '-o', 'example.png'])
Check the documentation for all available parameters
Licence & Contributors
This work is licenced under the MIT licence
Contributions are welcome!
Special thanks
@lukauskas for implementing i/o support for file-like objects.
@zfrenchee for fixing a bug in the calculation of the test statistic.
@pommy1 for implementing support for networkx >= 2.0.0.
Building the documentation
sphinx-apidoc -f -o docs goenrich goenrich/tests1 maintainer
Metadata
1 maintainer
Release files for goenrich 1.12
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