# ---------------------------------------------------------------------------- # 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. # ---------------------------------------------------------------------------- import io from unittest import TestCase, main from skbio import Protein, DNA, RNA, Sequence from skbio.metadata import IntervalMetadata from skbio.util import get_data_path from skbio.io import GenBankFormatError from skbio.io.format.genbank import ( _genbank_sniffer, _genbank_to_generator, _genbank_to_sequence, _genbank_to_dna, _genbank_to_rna, _genbank_to_protein, _parse_locus, _parse_reference, _generator_to_genbank, _sequence_to_genbank, _protein_to_genbank, _rna_to_genbank, _dna_to_genbank, _serialize_locus) class SnifferTests(TestCase): def setUp(self): self.positive_fps = list(map(get_data_path, [ 'genbank_5_blanks_start_of_file', 'genbank_single_record_upper', 'genbank_single_record_lower', 'genbank_multi_records'])) self.negative_fps = list(map(get_data_path, [ 'empty', 'whitespace_only', 'genbank_6_blanks_start_of_file', 'genbank_w_beginning_whitespace', 'genbank_missing_locus_name'])) def test_positives(self): for fp in self.positive_fps: self.assertEqual(_genbank_sniffer(fp), (True, {})) def test_negatives(self): for fp in self.negative_fps: self.assertEqual(_genbank_sniffer(fp), (False, {})) class GenBankIOTests(TestCase): # parent class to set up test data for the child class def setUp(self): # test locus line self.locus = ( (['LOCUS NC_005816 9609 bp ' 'DNA circular CON 07-FEB-2015'], {'division': 'CON', 'mol_type': 'DNA', 'shape': 'circular', 'locus_name': 'NC_005816', 'date': '07-FEB-2015', 'unit': 'bp', 'size': 9609}), (['LOCUS SCU49845 5028 bp ' 'DNA PLN 21-JUN-1999'], {'division': 'PLN', 'mol_type': 'DNA', 'shape': None, 'locus_name': 'SCU49845', 'date': '21-JUN-1999', 'unit': 'bp', 'size': 5028}), (['LOCUS NP_001832 360 aa ' 'linear PRI 18-DEC-2001'], {'division': 'PRI', 'mol_type': None, 'shape': 'linear', 'locus_name': 'NP_001832', 'date': '18-DEC-2001', 'unit': 'aa', 'size': 360})) # test single record and read uppercase sequence self.single_upper_fp = get_data_path('genbank_single_record_upper') self.single_lower_fp = get_data_path('genbank_single_record_lower') self.single = ( 'GSREILDFK', {'LOCUS': {'date': '23-SEP-1994', 'division': 'BCT', 'locus_name': 'AAB29917', 'mol_type': None, 'shape': 'linear', 'size': 9, 'unit': 'aa'}}, None, Protein) self.single_rna_fp = get_data_path('genbank_single_record') imd = IntervalMetadata(63) imd.add([(0, 63)], [(False, False)], {'db_xref': '"taxon:562"', 'mol_type': '"mRNA"', 'organism': '"Escherichia coli"', 'type': 'source', 'strand': '+', '__location': '1..63'}) imd.add([(0, 63)], [(False, True)], {'phase': 0, 'db_xref': ['"taxon:562"', '"taxon:561"'], '__location': '1..>63', 'strand': '+', 'note': '"alkaline phosphatase signal peptide"', 'protein_id': '"AAA23431.1"', 'transl_table': '11', 'translation': '"MKQSTIALAVLPLLFTPVTKA"', 'type': 'CDS'}) self.single_rna = ( 'gugaaacaaagcacuauugcacuggcugucuuaccguuacuguuuaccccugugacaaaagcc', {'ACCESSION': 'M14399', 'COMMENT': 'Original source text: E.coli, cDNA to mRNA.', 'DEFINITION': "alkaline phosphatase signal mRNA, 5' end.", 'KEYWORDS': 'alkaline phosphatase; signal peptide.', 'LOCUS': {'date': '26-APR-1993', 'division': 'BCT', 'locus_name': 'ECOALKP', 'mol_type': 'mRNA', 'shape': 'linear', 'size': 63, 'unit': 'bp'}, 'SOURCE': {'ORGANISM': 'Escherichia coli', 'taxonomy': 'Bacteria; Proteobacteria; ' 'Gammaproteobacteria; Enterobacteriales; ' 'Enterobacteriaceae; Escherichia.'}, 'VERSION': 'M14399.1'}, imd, RNA) # test: # 1. multiple records in one file # 2. lowercase sequence # 3. DNA, RNA, Protein type # 4. variation of formats self.multi_fp = get_data_path('genbank_multi_records') imd_pro = IntervalMetadata(9) imd_pro.add([(0, 9)], [(False, False)], {'organism': '"Bacteria"', 'type': 'source', 'strand': '+', '__location': '1..9'},) imd_pro.add([(0, 9)], [(False, True)], {'__location': '1..>9', 'product': '"L-carnitine amidase"', 'strand': '+', 'type': 'Protein'}) imd_dna = IntervalMetadata(9) imd_dna.add([(0, 9)], [(False, False)], {'country': '"Brazil: Parana, Paranavai"', 'type': 'source', 'strand': '+', '__location': '1..9', 'environmental_sample': ''}) imd_dna.add([(1, 8)], [(True, True)], {'__location': 'complement(<2..>8)', 'product': '"16S ribosomal RNA"', 'strand': '-', 'type': 'rRNA'}) self.multi = ( ('gsreildfk', {'ACCESSION': 'AAB29917', 'COMMENT': 'Method: direct peptide sequencing.', 'DBSOURCE': 'accession AAB29917.1', 'DEFINITION': 'L-carnitine amidase {N-terminal}', 'KEYWORDS': '.', 'LOCUS': {'date': '23-SEP-1994', 'division': 'BCT', 'locus_name': 'AAB29917', 'mol_type': None, 'shape': 'linear', 'size': 9, 'unit': 'aa'}, 'REFERENCE': [{'AUTHORS': 'Joeres,U. and Kula,M.R.', 'JOURNAL': 'AMB 40 (5), 606-610 (1994)', 'PUBMED': '7764422', 'REFERENCE': '1 (residues 1 to 9)', 'REMARK': 'from the original journal article.', 'TITLE': 'a microbial L-carnitine amidase'}, {'AUTHORS': 'Joeres,U. and Kula,M.R.', 'JOURNAL': 'AMB 40 (5), 606-610 (1994)', 'PUBMED': '7764422', 'REFERENCE': '1 (residues 1 to 9)', 'TITLE': 'a microbial L-carnitine amidase'}], 'SOURCE': {'ORGANISM': 'Bacteria', 'taxonomy': 'Unclassified.'}, 'VERSION': 'AAB29917.1 GI:545426'}, imd_pro, Protein), ('catgcaggc', {'ACCESSION': 'HQ018078', 'DEFINITION': 'Uncultured Xylanimonas sp.16S, partial', 'KEYWORDS': 'ENV.', 'LOCUS': {'date': '29-AUG-2010', 'division': 'ENV', 'locus_name': 'HQ018078', 'mol_type': 'DNA', 'shape': 'linear', 'size': 9, 'unit': 'bp'}, 'SOURCE': {'ORGANISM': 'uncultured Xylanimonas sp.', 'taxonomy': 'Bacteria; Actinobacteria; ' 'Micrococcales; Promicromonosporaceae; ' 'Xylanimonas; environmental samples.'}, 'VERSION': 'HQ018078.1 GI:304421728'}, imd_dna, DNA)) class ReaderTests(GenBankIOTests): def test_parse_reference(self): lines = ''' REFERENCE 1 (bases 1 to 154478) AUTHORS Sato,S., Nakamura,Y., Kaneko,T., and Tabata,S. TITLE Complete structure of the chloroplast genome of Arabidopsis thaliana JOURNAL DNA Res. 6 (5), 283-290 (1999) PUBMED 10574454'''.split('\n') exp = {'AUTHORS': 'Sato,S., Nakamura,Y., Kaneko,T., and Tabata,S.', 'JOURNAL': 'DNA Res. 6 (5), 283-290 (1999)', 'PUBMED': '10574454', 'REFERENCE': '1 (bases 1 to 154478)', 'TITLE': ('Complete structure of the chloroplast genome of' ' Arabidopsis thaliana')} self.assertEqual(_parse_reference(lines), exp) def test_parse_locus(self): for serialized, parsed in self.locus: self.assertEqual(_parse_locus(serialized), parsed) def test_parse_locus_invalid(self): lines = [ # missing unit ['LOCUS NC_005816 9609 ' ' DNA circular CON 07-FEB-2015'], # missing division ['LOCUS SCU49845 5028 bp' ' DNA 21-JUN-1999'], # wrong date format ['LOCUS NP_001832 360 aa' ' linear PRI 2001-12-18']] for line in lines: with self.assertRaisesRegex(GenBankFormatError, r'Could not parse the LOCUS line:.*'): _parse_locus(line) def test_genbank_to_generator_single(self): # test single record and uppercase sequence for c in [Sequence, Protein]: obs = next(_genbank_to_generator( self.single_upper_fp, constructor=c)) exp = c(self.single[0], metadata=self.single[1], positional_metadata=self.single[2]) self.assertEqual(exp, obs) def test_genbank_to_generator(self): for i, obs in enumerate(_genbank_to_generator(self.multi_fp)): seq, md, imd, constructor = self.multi[i] exp = constructor(seq, metadata=md, lowercase=True, interval_metadata=imd) self.assertEqual(exp, obs) def test_genbank_to_sequence(self): for i, exp in enumerate(self.multi): obs = _genbank_to_sequence(self.multi_fp, seq_num=i+1) exp = Sequence(exp[0], metadata=exp[1], lowercase=True, interval_metadata=exp[2]) self.assertEqual(exp, obs) def test_genbank_to_rna(self): seq, md, imd, constructor = self.single_rna obs = _genbank_to_rna(self.single_rna_fp) exp = constructor(seq, metadata=md, lowercase=True, interval_metadata=imd) self.assertEqual(exp, obs) def test_genbank_to_dna(self): i = 1 exp = self.multi[i] obs = _genbank_to_dna(self.multi_fp, seq_num=i+1) exp = DNA(exp[0], metadata=exp[1], lowercase=True, interval_metadata=exp[2]) self.assertEqual(exp, obs) def test_genbank_to_protein(self): i = 0 exp = self.multi[i] obs = _genbank_to_protein(self.multi_fp, seq_num=i+1) exp = Protein(exp[0], metadata=exp[1], lowercase=True, interval_metadata=exp[2]) self.assertEqual(exp, obs) class WriterTests(GenBankIOTests): def test_serialize_locus(self): for serialized, parsed in self.locus: self.assertEqual( _serialize_locus('LOCUS', parsed), serialized[0] + '\n') def test_generator_to_genbank(self): seq, md, imd, constructor = self.single obj = constructor(seq, md, interval_metadata=imd) with io.StringIO() as fh: _generator_to_genbank([obj], fh) obs = fh.getvalue() with open(self.single_lower_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) def test_sequence_to_genbank(self): with io.StringIO() as fh: for i, (seq, md, imd, constructor) in enumerate(self.multi): obj = Sequence(seq, md, interval_metadata=imd, lowercase=True) _sequence_to_genbank(obj, fh) obs = fh.getvalue() with open(self.multi_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) def test_dna_protein_to_genbank(self): writers = [_protein_to_genbank, _dna_to_genbank] with io.StringIO() as fh: for i, (seq, md, imd, constructor) in enumerate(self.multi): obj = constructor( seq, md, interval_metadata=imd, lowercase=True) writers[i](obj, fh) obs = fh.getvalue() with open(self.multi_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) def test_rna_to_genbank(self): with io.StringIO() as fh: seq, md, imd, constructor = self.single_rna obj = constructor(seq, md, interval_metadata=imd, lowercase=True) _rna_to_genbank(obj, fh) obs = fh.getvalue() with open(self.single_rna_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) class RoundtripTests(GenBankIOTests): def test_roundtrip_generator(self): with io.StringIO() as fh: _generator_to_genbank(_genbank_to_generator(self.multi_fp), fh) obs = fh.getvalue() with open(self.multi_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) def test_roundtrip_rna(self): with io.StringIO() as fh: _rna_to_genbank(_genbank_to_rna(self.single_rna_fp), fh) obs = fh.getvalue() with open(self.single_rna_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) def test_roundtrip_dna(self): with io.StringIO() as fh: _dna_to_genbank(_genbank_to_dna(self.single_rna_fp), fh) obs = fh.getvalue() with open(self.single_rna_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) def test_roundtrip_protein(self): with io.StringIO() as fh: _protein_to_genbank(_genbank_to_protein(self.single_lower_fp), fh) obs = fh.getvalue() with open(self.single_lower_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) def test_roundtrip_sequence(self): with io.StringIO() as fh: _sequence_to_genbank(_genbank_to_sequence(self.single_rna_fp), fh) obs = fh.getvalue() with open(self.single_rna_fp) as fh: exp = fh.read() self.assertEqual(obs, exp) if __name__ == '__main__': main()