def test_dbxref_feature_mapper():
'It tests the dbxref feature mapper'
database = 'database'
relations = {'ctg0': 'acc1'}
feature = {'end': 140722177, 'name': 'ctg0', 'start': 1,
'source': 'F=PC', 'seqid': 'Chrctg0', 'phase': '.',
'attributes': {'ID': 'ctg0', 'Name': 'ctg,0'},
'score': '.', 'type': 'contig', 'id':'ctg0', 'strand': '.'}
mapper = create_dbxref_adder(database, relations)
mapper((FEATURE, feature))
# add an already given database
mapper((FEATURE, feature))
assert feature['attributes']['Dbxref'] == ['database:acc1']
# add a second dbxref
mapper = create_dbxref_adder('database2', relations)
mapper((FEATURE, feature))
assert feature['attributes']['Dbxref'] == ['database2:acc1', 'database:acc1']
feature = {'end': 140722177, 'name': 'test', 'start': 1,
'source': 'F=PC', 'seqid': 'Chrctg0', 'phase': '.',
'attributes': {'ID': 'test', 'Name': 'test'},
'score': '.', 'type': 'contig', 'id':'test', 'strand': '.'}
mapper = create_dbxref_adder('database2', relations)
mapper((FEATURE, feature))
assert 'Dbxref' not in feature['attributes']
def main():
'It runs the script'
ingff3_fpath, outgff3_fpath, rels_fhand, database = get_parameters()
relations = _get_relations(rels_fhand)
mappers = []
mappers.append(create_dbxref_adder(database, relations))
modify_gff3(ingff3_fpath, outgff3_fpath, mappers=mappers)
