goatools.anno.init.reader_genetogo module¶

Read an NCBI gene2go GO Association File and store the data in a Python object.

Annotations available from NCBI:: ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz

class goatools.anno.init.reader_genetogo.InitAssc(taxid=None, taxids=None)[source]¶

Bases: object

Read annotation file and store a list of namedtuples.

taxid_dflt = 9606¶

hdrs = ['tax_id', 'GeneID', 'GO_ID', 'Evidence', 'Qualifier', 'GO_term', 'PubMed', 'Category']¶

flds = ['tax_id', 'DB_ID', 'GO_ID', 'Evidence_Code', 'Qualifier', 'GO_term', 'DB_Reference', 'NS']¶

init_associations(fin_anno, taxids=None, namespaces=None)[source]¶: Read annotation file. Store annotation data in a list of namedtuples.