goatools.evidence_codes module

Manage evidence codes as reported by the Gene Ontology Consortium.

class goatools.evidence_codes.EvidenceCodes

Bases: object

From http://geneontology.org/page/guide-go-evidence-codes

ntobj

alias of NtCode

code2nt = {'EXP': ('ECO:0000269', 'Experimental', 'Inferred from Experiment'), 'HDA': ('ECO:0007005', 'High_Throughput', 'Inferred from High Throughput Direct Assay'), 'HEP': ('ECO:0007007', 'High_Throughput', 'Inferred from High Throughput Expression Pattern'), 'HGI': ('ECO:0007003', 'High_Throughput', 'Inferred from High Throughput Genetic Interaction'), 'HMP': ('ECO:0007001', 'High_Throughput', 'Inferred from High Throughput Mutant Phenotype'), 'HTP': ('ECO:0006056', 'High_Throughput', 'Inferred from High Throughput Experimental'), 'IBA': ('ECO:0000318', 'Similarity', 'Inferred from Biological aspect of Ancestor'), 'IBD': ('ECO:0000319', 'Similarity', 'Inferred from Biological aspect of Descendant'), 'IC': ('ECO:0000305', 'Curatorial', 'Inferred by Curator'), 'IDA': ('ECO:0000314', 'Experimental', 'Inferred from Direct Assay'), 'IEA': ('ECO:0000501', 'Automatic', 'Inferred from Electronic Annotation'), 'IEP': ('ECO:0000270', 'Experimental', 'Inferred from Expression Pattern'), 'IGC': ('ECO:0000317', 'Similarity', 'Inferred from Genomic Context'), 'IGI': ('ECO:0000316', 'Experimental', 'Inferred from Genetic Interaction'), 'IKR': ('ECO:0000320', 'Similarity', 'Inferred from phylogenetic determination of loss of key residues (manual assertion)'), 'IMP': ('ECO:0000315', 'Experimental', 'Inferred from Mutant Phenotype'), 'IMR': ('ECO:0000320', 'Similarity', 'Phylogenetic determination of loss of key residues in manual assertion'), 'IPI': ('ECO:0000353', 'Experimental', 'Inferred from Physical Interaction'), 'IRD': ('ECO:0000321', 'Similarity', 'Inferred from Rapid Divergence from ancestral sequence (manual assertion)'), 'ISA': ('ECO:0000247', 'Similarity', 'Inferred from Sequence Alignment'), 'ISM': ('ECO:0000255', 'Similarity', 'Inferred from Sequence Model used in manual assertion'), 'ISO': ('ECO:0000266', 'Similarity', 'Inferred from Sequence Orthology'), 'ISS': ('ECO:0000250', 'Similarity', 'Inferred from Sequence or structural Similarity'), 'NAS': ('ECO:0000303', 'Author', 'Non-traceable Author Statement used in manual assertion'), 'ND': ('ECO:0000307', 'No biological data', 'No biological Data available'), 'RCA': ('ECO:0000245', 'Combinatorial', 'Inferred from Reviewed Computational Analysis'), 'TAS': ('ECO:0000304', 'Author', 'Traceable Author Statement used in manual assertion')}

ev2idx = {'EXP': 0, 'HDA': 18, 'HEP': 21, 'HGI': 20, 'HMP': 19, 'HTP': 17, 'IBA': 11, 'IBD': 12, 'IC': 24, 'IDA': 1, 'IEA': 26, 'IEP': 5, 'IGC': 10, 'IGI': 4, 'IKR': 13, 'IMP': 3, 'IMR': 15, 'IPI': 2, 'IRD': 14, 'ISA': 8, 'ISM': 9, 'ISO': 7, 'ISS': 6, 'NAS': 23, 'ND': 25, 'RCA': 16, 'TAS': 22}

prt_summary_code(prt=sys.stdout)

Print summary of codes and groups that can be inputs to get_evcodes.

prt_details(prt=sys.stdout)

Print summary of codes and groups that can be inputs to get_evcodes.

get_min_inc_exc(inc_set=None, exc_set=None)

Get the user-specified Evidence codes. Return smaller set: include/exclude

get_evcodes(inc_set=None, exc_set=None)

Get evidence code for all but NOT ‘No biological data’

get_evcodes_all(inc_set=None, exc_set=None)

Get set of evidence codes given include set and exclude set

sort_nts(nt_list, codekey)

Sort list of namedtuples such so evidence codes in same order as code2nt.

get_grp_name(code)

Return group and name for an evidence code.

prt_ev_cnts(ctr, prt=sys.stdout)

Prints evidence code counts stored in a collections Counter.

get_order(codes)

Return evidence codes in order shown in code2name.

prt_summary_anno2ev(associations, prt=sys.stdout)

Print annotation/evidence code summary.