goenrich 1.11

安装

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.gz

运行go浓缩

importgoenrich# build the ontologyO=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 yeastgene2go=goenrich.read.gene2go('db/gene2go.gz')# use values = {k: set(v) for k,v in annot.groupby('go_id')['db_object_symbol']} for uniprot/yeastvalues={k:set(v)fork,vingene2go.groupby('GO_ID')['GeneID']}# propagate the background through the ontologybackground_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 smalldf=goenrich.enrich.analyze(O,query,background_attribute,gvfile='test.dot')# generate htmldf.dropna().head().to_html('example.html')# call to graphvizimportsubprocesssubprocess.check_call(['dot','-Tpng','test.dot','-o','test.png'])

使用graphviz生成png图像：

dot -Tpng example.dot > example.png

或者直接从python：

importsubprocesssubprocess.check_call(['dot','-Tpng','example.dot','-o','example.png'])

查看文档以了解所有可用参数

特别感谢

• @lukauskas用于实现对类文件对象的I/O支持。
• @zfrenchee用于在测试统计量的计算中修正bug。
• @pommy1用于实现对networkx >= 2.0.0的支持。