goatools.associations module¶
Routines to read in association file between genes and GO terms.
- goatools.associations.dnld_assc(assc_name, go2obj=None, namespace='BP', prt=sys.stdout)[source]¶
Download association from http://geneontology.org/gene-associations.
- goatools.associations.dnld_annotation(assc_file, prt=sys.stdout)[source]¶
Download gaf, gpad, or gpi from http://current.geneontology.org/annotations/
- goatools.associations.read_associations(assoc_fn, anno_type='id2gos', namespace='BP', **kws)[source]¶
Return associatinos in id2gos format
- goatools.associations.get_assoc_ncbi_taxids(taxids, force_dnld=False, **kws)[source]¶
Download NCBI’s gene2go. Return annotations for user-specified taxid(s).
- goatools.associations.dnld_ncbi_gene_file(fin, force_dnld=False, log=sys.stdout)[source]¶
Download a file from NCBI Gene’s ftp server.
- goatools.associations.dnld_annofile(fin_anno, anno_type)[source]¶
Download annotation file, if needed
- goatools.associations.read_ncbi_gene2go(fin_gene2go, taxids=None, namespace='BP', **kws)[source]¶
Read NCBI’s gene2go. Return gene2go data for user-specified taxids.
- goatools.associations.get_gaf_hdr(fin_gaf)[source]¶
Read Gene Association File (GAF). Return GAF version and data info.
- goatools.associations.read_gaf(fin_gaf, prt=sys.stdout, hdr_only=False, namespace='BP', allow_missing_symbol=False, **kws)[source]¶
Read Gene Association File (GAF). Return data.
- goatools.associations.get_b2aset(a2bset)[source]¶
Given gene2gos, return go2genes. Given go2genes, return gene2gos.
- goatools.associations.get_assc_pruned(assc_geneid2gos, min_genecnt=None, max_genecnt=None, prt=sys.stdout)[source]¶
Remove GO IDs associated with large numbers of genes. Used in stochastic simulations.