def test_feature_type_filter():
'It tests the dbxref feature mapper'
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': '.'}
type_filter = create_feature_type_filter(['contig'])
assert filter(type_filter, [(FEATURE, feature)])
type_filter = create_feature_type_filter(['gene'])
assert not filter(type_filter, [(FEATURE, feature)])
def test_gff_filters(self):
'It test that we can use filters for features in gff'
types = ['gene']
gff_fhand = NamedTemporaryFile()
gff_fhand.write(GFF_CONTENT)
gff_fhand.flush()
type_filter = create_feature_type_filter(types)
gff = GffFile(fpath=gff_fhand.name)
items = filter(type_filter, gff.items)
assert items[1][1]['id'] == 'gene00001'
types = ['contig']
type_filter = create_feature_type_filter(types)
gff = GffFile(fpath=gff_fhand.name)
items = filter(type_filter, gff.items)
assert len(items) == 2
def main():
'It runs the script'
ingff3_fpath, outgff3_fpath, types = get_parameters()
filters = []
filters.append(create_feature_type_filter(types))
modify_gff(ingff3_fpath, outgff3_fpath, filters=filters)