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
pandasfor processing andgraphvizfor visualization
Install package from pypi and download ontology
and needed annotations.
and needed annotations.
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/gene_association.goa_ref_human.gz -O db/gene_association.goa_ref_human.gz
# Entrez GeneID
wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz -O db/gene2go.gzimport goenrich
# build the ontology
O = goenrich.obo.ontology('db/go-basic.obo')
# use all entrez geneid associations form gene2go as background
# use goenrich.read.goa('db/gene_association.goa_ref_human.gz') for uniprot
gene2go = goenrich.read.gene2go('db/gene2go.gz')
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
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'])| name | namespace | p | q | rejected | term | |
|---|---|---|---|---|---|---|
| 1245 | response to organic cyclic compound | biological_process | 2.856257e-06 | 6.732606e-06 | 1 | GO:0014070 |
| 1668 | ATP binding | molecular_function | 8.821334e-09 | 3.325412e-07 | 1 | GO:0005524 |
| 1988 | phosphorylation | biological_process | 1.101491e-03 | 1.118437e-03 | 1 | GO:0016310 |
| 3319 | cellular response to organonitrogen compound | biological_process | 2.639774e-05 | 5.084590e-05 | 1 | GO:0071417 |
| 3422 | metal ion binding | molecular_function | 1.719726e-05 | 3.439452e-05 | 1 | GO:0046872 |
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
This work is licenced under the MIT licence
Contributions are welcome!
sphinx-apidoc -f -o docs goenrich goenrich/tests