goatools.anno.dnld_ebi_goa module

Download GOA files from the Gene Ontology Annotation (GOA) resource http://www.ebi.ac.uk/GOA.

class goatools.anno.dnld_ebi_goa.DnldGoa

Bases: object

Download files from the Gene Ontology Annotation (GOA) resource http://www.ebi.ac.uk/GOA.

ftp_pub = 'ftp://ftp.ebi.ac.uk/pub/'

species = ['arabidopsis', 'chicken', 'cow', 'dicty', 'dog', 'fly', 'human', 'mouse', 'pig', 'rat', 'uniprot', 'worm', 'yeast', 'zebrafish']

species_items = ['complex', 'isoform', 'rna']

exts = ['gaf', 'gpa', 'gpi']

dnld_goa(species, ext='gaf', item=None, fileout=None)

Download GOA source file name on EMBL-EBI ftp server.

get_basename(species, ext='gaf', item=None)

Get GOA basename for a specific species. Ex: goa_human.gaf