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# ----------------------------------------------------------------------------
# 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()
|
