# ---------------------------------------------------------------------------- # Copyright (c) 2013--, scikit-bio development team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file COPYING.txt, distributed with this software. # ---------------------------------------------------------------------------- from unittest import TestCase, main import io from skbio.util import get_data_path from skbio.metadata import IntervalMetadata from skbio import DNA, Sequence from skbio.io import GFF3FormatError from skbio.io.format.gff3 import (_yield_record, _parse_record, _parse_attr, _gff3_sniffer, _gff3_to_interval_metadata, _interval_metadata_to_gff3, _gff3_to_generator, _generator_to_gff3, _gff3_to_sequence, _sequence_to_gff3, _gff3_to_dna, _dna_to_gff3, _serialize_interval_metadata) class GFF3IOTests(TestCase): def setUp(self): self.multi_fp = get_data_path('gff3_multi_record') self.single_fp = get_data_path('gff3_single_record') intvls = [{'bounds': [(0, 4641652)], 'metadata': {'source': 'European Nucleotide Archive', 'type': 'chromosome', 'score': '.', 'strand': '.', 'ID': 'chromosome:Chromosome', 'Alias': 'U00096.3', 'Is_circular': 'true'}}, {'bounds': [(147, 148)], 'metadata': {'source': 'regulondb_feature', 'type': 'biological_region', 'score': '.', 'strand': '+', 'external_name': 'Promoter thrLp (RegulonDB:ECK120010236)', 'logic_name': 'regulondb_promoter'}}, {'bounds': [(336, 2799)], 'metadata': {'source': 'Prodigal_v2.60', 'type': 'gene', 'score': '1.8', 'strand': '+', 'phase': 0, 'ID': '1_1', 'gc_cont': '0.427'}}, {'bounds': [(336, 2799)], 'metadata': {'source': 'Prodigal_v2.60', 'type': 'CDS', 'score': '333.8', 'strand': '+', 'phase': 0, 'ID': '1_2', 'Parent': '1_1', 'rbs_motif': 'GGAG/GAGG', 'rbs_spacer': '5-10bp'}}, {'bounds': [(0, 50), (55, 100)], 'metadata': {'source': 'Prodigal_v2.60', 'type': 'gene', 'score': '1.8', 'strand': '+', 'phase': 0, 'ID': '1_1', 'gene': 'FXR receptor'}}] self.upper_bound = 4641652 self.imd1 = IntervalMetadata(self.upper_bound) self.imd1.add(**intvls[0]) self.imd1.add(**intvls[1]) self.imd2 = IntervalMetadata(None) self.imd2.add(**intvls[2]) self.imd2.add(**intvls[3]) self.imd3 = IntervalMetadata(None) self.imd3.add(**intvls[4]) self.seq_fp = get_data_path('gff3_dna') self.seq = Sequence('ATGCATGCATGC', metadata={'id': 'NC_1', 'description': 'species X'}) self.seq.interval_metadata.add( [(0, 9)], metadata={'source': 'Prodigal_v2.60', 'type': 'gene', 'score': '.', 'strand': '+', 'phase': 0, 'ID': 'gene1', 'Name': 'FXR'}) self.dna = DNA(self.seq) class SnifferTests(TestCase): def setUp(self): self.positive_fps = map(get_data_path, [ 'gff3_multi_record', 'gff3_single_record', 'gff3_dna']) self.negative_fps = map(get_data_path, [ 'empty', 'whitespace_only', 'gff3_bad_missing_directive']) def test_positive(self): for fp in self.positive_fps: self.assertEqual(_gff3_sniffer(fp), (True, {})) def test_negative(self): for fp in self.negative_fps: self.assertEqual(_gff3_sniffer(fp), (False, {})) class ReaderTests(GFF3IOTests): def test_parse_attr(self): s = 'Dbxref=GO:000152,GO:001234;Note=fooo' obs = _parse_attr(s) exp = {'db_xref': 'GO:000152,GO:001234', 'note': 'fooo'} self.assertEqual(exp, obs) def test_yield_record(self): obs = [('data', 'seqid1', ['seqid1\txxx', 'seqid1\tyyy']), ('data', 'seqid2', ['seqid2\tzzz'])] s = ('seqid1\txxx\n' 'seqid1\tyyy\n' 'seqid2\tzzz\n') fh = io.StringIO(s) for i, j in zip(_yield_record(fh), obs): self.assertEqual(i, j) def test_parse_record_raise(self): chars = 'abc?!' for char in chars: lines = [ 'ctg123\t.\tgene\t1000\t9000\t.\t+\t%s\tID=gene00001' % char] with self.assertRaisesRegex( GFF3FormatError, r"unknown value for phase column: '%s'" % char): _parse_record(lines, 10000) def test_yield_record_raise(self): s = '##gff-version 3\nseq_1 . gene 1 3 . + . ID=gene01\n' with io.StringIO(s) as fh: with self.assertRaises(GFF3FormatError): list(_yield_record(fh)) def test_gff3_to_interval_metadata(self): obs = _gff3_to_interval_metadata( self.single_fp, seq_id='Chromosome') self.assertEqual(obs, self.imd1) def test_gff3_to_interval_metadata_empty(self): exp = IntervalMetadata(None) obs = _gff3_to_interval_metadata( # the seq id does not exist self.single_fp, seq_id='foo') self.assertEqual(obs, exp) def test_gff3_to_interval_metadata_bad(self): with self.assertRaisesRegex(GFF3FormatError, r'do not have 9 columns in this line'): _gff3_to_interval_metadata( get_data_path('gff3_bad_wrong_columns'), seq_id='Chromosome') def test_gff3_to_generator(self): exps = [('Chromosome', self.imd1), ('gi|556503834|ref|NC_000913.3|', self.imd2)] obss = _gff3_to_generator(self.multi_fp) for obs, exp in zip(obss, exps): self.assertEqual(obs, exp) def test_gff3_to_generator_empty(self): empty_fps = map(get_data_path, ['empty', 'whitespace_only']) for empty_fp in empty_fps: obs = list(_gff3_to_generator(empty_fp)) self.assertEqual(obs, []) def test_gff3_to_sequence(self): obs = _gff3_to_sequence(self.seq_fp) self.assertEqual(obs, self.seq) def test_gff3_to_dna(self): obs = _gff3_to_dna(self.seq_fp) self.assertEqual(obs, self.dna) class WriterTests(GFF3IOTests): def test_interval_metadata_to_gff3(self): with io.StringIO() as fh: _interval_metadata_to_gff3(self.imd1, fh, seq_id='Chromosome') # only compare the uncommented lines because the comments are not # stored in IntervalMetadata obs = [i for i in fh.getvalue().splitlines() if not i.startswith('#')] with open(self.single_fp) as f: exp = [i.rstrip() for i in f.readlines() if not i.startswith('#')] self.assertEqual(obs, exp) def test_interval_metadata_to_gff3_missing_field(self): exp = 'ctg123\t.\tgene\t1\t9\t.\t.\t.\tID=gene00001;Name=EDEN' imd = IntervalMetadata(9) imd.add([(0, 9)], metadata={ 'type': 'gene', 'ID': 'gene00001', 'Name': 'EDEN'}) with io.StringIO() as fh: _interval_metadata_to_gff3(imd, fh, seq_id='ctg123') # only compare the uncommented lines because the comments are not # stored in IntervalMetadata obs = [i for i in fh.getvalue().splitlines() if not i.startswith('#')] self.assertEqual([exp], obs) def test_interval_metadata_to_gff3_escape(self): # test escape of reserved char in GFF3 exp = 'ctg123\t.\tgene\t1\t9\t.\t.\t.\tID=a%3B%3D%26%2Cb' imd = IntervalMetadata(9) imd.add([(0, 9)], metadata={ 'type': 'gene', 'ID': 'a;=&,b'}) with io.StringIO() as fh: _interval_metadata_to_gff3(imd, fh, seq_id='ctg123') # only compare the uncommented lines because the comments are not # stored in IntervalMetadata obs = [i for i in fh.getvalue().splitlines() if not i.startswith('#')] self.assertEqual([exp], obs) def test_interval_metadata_to_gff3_multiple_values(self): # test multiple values of db_xref are correctly serialized exp = 'ctg123\t.\tgene\t1\t9\t.\t.\t.\tDbxref=GO:000152,GO:001234' imd = IntervalMetadata(9) imd.add([(0, 9)], metadata={ 'type': 'gene', 'db_xref': ['GO:000152', 'GO:001234']}) with io.StringIO() as fh: _interval_metadata_to_gff3(imd, fh, seq_id='ctg123') # only compare the uncommented lines because the comments are not # stored in IntervalMetadata obs = [i for i in fh.getvalue().splitlines() if not i.startswith('#')] self.assertEqual([exp], obs) def test_interval_metadata_to_gff3_empty(self): imd = IntervalMetadata(None) with io.StringIO() as fh: _interval_metadata_to_gff3(imd, fh, seq_id='foo') obs = fh.getvalue() self.assertEqual(obs, '##gff-version 3\n') def test_interval_metadata_to_gff3_sub_region(self): seq_id = 'NC 7' with open(self.multi_fp) as f: exp = [i.strip() for i in f if i.startswith(seq_id)] with io.StringIO() as fh: _serialize_interval_metadata( self.imd3, seq_id=seq_id, fh=fh, skip_subregion=False) obs = [i for i in fh.getvalue().splitlines() if not i.startswith('#')] self.assertEqual(exp, obs) with io.StringIO() as fh: _serialize_interval_metadata(self.imd3, seq_id=seq_id, fh=fh) obs = [i for i in fh.getvalue().splitlines() if not i.startswith('#')] # all the rest lines except the 1st are sub-region lines, so only # compare the first line from exp self.assertEqual(exp[:1], obs) def test_sequence_to_gff3(self): with io.StringIO() as fh: _sequence_to_gff3(self.seq, fh) obs = fh.getvalue() with open(self.seq_fp) as fh: exp = fh.read() self.assertEqual(exp, obs) def test_dna_to_gff3(self): with io.StringIO() as fh: _dna_to_gff3(self.dna, fh) obs = fh.getvalue() with open(self.seq_fp) as fh: exp = fh.read() self.assertEqual(exp, obs) def test_raise_subregion(self): im = IntervalMetadata(None) im.add([(0, 3), (7, 9)], metadata={'type': 'gene'}) with io.StringIO() as fh: with self.assertRaises(GFF3FormatError): _serialize_interval_metadata( im, seq_id='a', fh=fh, skip_subregion=False) class RoundtripTests(GFF3IOTests): def test_roundtrip_interval_metadata(self): '''''' with io.StringIO() as fh: _interval_metadata_to_gff3( _gff3_to_interval_metadata( self.single_fp, seq_id='Chromosome'), fh, seq_id='Chromosome') obs = [i for i in fh.getvalue().splitlines() if not i.startswith('#')] with open(self.single_fp) as f: exp = [i.rstrip() for i in f.readlines() if not i.startswith('#')] self.assertEqual(obs, exp) def test_roundtrip_interval_metadata_generator(self): with io.StringIO() as fh: _generator_to_gff3( _gff3_to_generator(self.multi_fp), fh, skip_subregion=False) obs = [i for i in fh.getvalue().splitlines() if not i.startswith('#')] with open(self.multi_fp) as f: exp = [i.rstrip() for i in f.readlines() if not i.startswith('#')] self.assertEqual(obs, exp) if __name__ == '__main__': main()