def setUp(self):
self.pynast_test1_input_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='.fasta')
open(self.pynast_test1_input_fp, 'w').write(pynast_test1_input_fasta)
self.pynast_test1_template_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='template.fasta')
open(self.pynast_test1_template_fp, 'w').\
write(pynast_test1_template_fasta)
self.pynast_test_template_w_dots_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='template.fasta')
open(self.pynast_test_template_w_dots_fp, 'w').\
write(pynast_test1_template_fasta.replace('-', '.'))
self.pynast_test_template_w_u_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='template.fasta')
open(self.pynast_test_template_w_u_fp, 'w').\
write(pynast_test1_template_fasta.replace('T', 'U'))
self.pynast_test_template_w_lower_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='template.fasta')
open(self.pynast_test_template_w_lower_fp, 'w').\
write(pynast_test1_template_fasta.lower())
# create temp file names (and touch them so we can reliably
# clean them up)
self.result_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='.fasta')
open(self.result_fp, 'w').close()
self.failure_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='.fasta')
open(self.failure_fp, 'w').close()
self.log_fp = get_tmp_filename(
prefix='PyNastAlignerTests_', suffix='.log')
open(self.log_fp, 'w').close()
self._paths_to_clean_up = [
self.pynast_test1_input_fp,
self.result_fp,
self.failure_fp,
self.log_fp,
self.pynast_test1_template_fp,
self.pynast_test_template_w_dots_fp,
self.pynast_test_template_w_u_fp,
self.pynast_test_template_w_lower_fp
]
self.pynast_test1_aligner = PyNastAligner({
'template_filepath': self.pynast_test1_template_fp,
'min_len': 15,
})
self.pynast_test1_expected_aln = \
LoadSeqs(
data=pynast_test1_expected_alignment,
aligned=DenseAlignment)
self.pynast_test1_expected_fail = \
LoadSeqs(data=pynast_test1_expected_failure, aligned=False)
def test_call_pynast_template_aln_with_U(self):
"""PyNastAligner: error message when template contains bad char
"""
pynast_aligner = PyNastAligner({
'template_filepath': self.pynast_test_template_w_u_fp,
'min_len': 15,
})
self.assertRaises(KeyError, pynast_aligner, self.pynast_test1_input_fp)
def test_call_pynast_alt_pairwise_method(self):
"""PyNastAligner: alternate pairwise alignment method produces correct alignment
"""
aligner = PyNastAligner({
'pairwise_alignment_method': 'muscle',
'template_filepath': self.pynast_test1_template_fp,
'min_len': 15,
})
actual_aln = aligner(self.pynast_test1_input_fp)
expected_aln = self.pynast_test1_expected_aln
self.assertEqual(actual_aln, expected_aln)
def test_call_pynast_test1_alt_min_len(self):
"""PyNastAligner: returns no result when min_len too high
"""
aligner = PyNastAligner({
'template_filepath': self.pynast_test1_template_fp,
'min_len': 1000
})
actual_aln = aligner(self.pynast_test1_input_fp)
expected_aln = Alignment([])
self.assertEqual(actual_aln, expected_aln)
def test_call_pynast_template_aln_with_lower(self):
"""PyNastAligner: functions when template alignment contains lower case
"""
pynast_aligner = PyNastAligner({
'template_filepath': self.pynast_test_template_w_lower_fp,
'min_len': 15,
})
actual_aln = pynast_aligner(self.pynast_test1_input_fp)
expected_aln = self.pynast_test1_expected_aln
expected_names = ['1 description field 1..23', '2 1..23']
self.assertEqual(actual_aln.Names, expected_names)
self.assertEqual(actual_aln, expected_aln)
def test_call_pynast_test1_file_output_alt_params(self):
"""PyNastAligner writes correct output files when no seqs align
"""
aligner = PyNastAligner({
'template_filepath': self.pynast_test1_template_fp,
'min_len': 1000})
actual = aligner(
self.pynast_test1_input_fp, result_path=self.result_fp,
log_path=self.log_fp, failure_path=self.failure_fp)
self.assertTrue(actual is None,
"Result should be None when result path provided.")
self.assertEqual(getsize(self.result_fp), 0,
"No alignable seqs should result in an empty file.")
# all seqs reported to fail
actual_fail = LoadSeqs(self.failure_fp, aligned=False)
self.assertEqual(actual_fail.getNumSeqs(), 3)
def test_call_pynast_test1_file_output_alt_params(self):
"""PyNastAligner writes correct output files when no seqs align
"""
aligner = PyNastAligner({
'template_filepath': self.pynast_test1_template_fp,
'min_len': 1000})
actual = aligner(
self.pynast_test1_input_fp, result_path=self.result_fp,
log_path=self.log_fp, failure_path=self.failure_fp)
self.assertTrue(actual is None,
"Result should be None when result path provided.")
self.assertEqual(getsize(self.result_fp), 0,
"No alignable seqs should result in an empty file.")
# all seqs reported to fail
with open(self.failure_fp) as failure_f:
actual_fail = SequenceCollection.from_fasta_records(
parse_fasta(failure_f), DNA)
self.assertEqual(actual_fail.sequence_count(), 3)
def setUp(self):
fd, self.pynast_test1_input_fp = mkstemp(prefix='PyNastAlignerTests_',
suffix='.fasta')
close(fd)
with open(self.pynast_test1_input_fp, 'w') as f:
f.write(pynast_test1_input_fasta)
fd, self.pynast_test1_template_fp = mkstemp(
prefix='PyNastAlignerTests_', suffix='template.fasta')
close(fd)
with open(self.pynast_test1_template_fp, 'w') as f:
f.write(pynast_test1_template_fasta)
fd, self.pynast_test_template_w_dots_fp = mkstemp(
prefix='PyNastAlignerTests_', suffix='template.fasta')
close(fd)
with open(self.pynast_test_template_w_dots_fp, 'w') as f:
f.write(pynast_test1_template_fasta.replace('-', '.'))
fd, self.pynast_test_template_w_u_fp = mkstemp(
prefix='PyNastAlignerTests_', suffix='template.fasta')
close(fd)
with open(self.pynast_test_template_w_u_fp, 'w') as f:
f.write(pynast_test1_template_fasta.replace('T', 'U'))
fd, self.pynast_test_template_w_lower_fp = mkstemp(
prefix='PyNastAlignerTests_', suffix='template.fasta')
close(fd)
with open(self.pynast_test_template_w_lower_fp, 'w') as f:
f.write(pynast_test1_template_fasta.lower())
# create temp file names (and touch them so we can reliably
# clean them up)
fd, self.result_fp = mkstemp(prefix='PyNastAlignerTests_',
suffix='.fasta')
close(fd)
open(self.result_fp, 'w').close()
fd, self.failure_fp = mkstemp(prefix='PyNastAlignerTests_',
suffix='.fasta')
close(fd)
open(self.failure_fp, 'w').close()
fd, self.log_fp = mkstemp(prefix='PyNastAlignerTests_', suffix='.log')
close(fd)
open(self.log_fp, 'w').close()
self._paths_to_clean_up = [
self.pynast_test1_input_fp, self.result_fp, self.failure_fp,
self.log_fp, self.pynast_test1_template_fp,
self.pynast_test_template_w_dots_fp,
self.pynast_test_template_w_u_fp,
self.pynast_test_template_w_lower_fp
]
self.pynast_test1_aligner = PyNastAligner({
'template_filepath': self.pynast_test1_template_fp,
'min_len': 15,
})
self.pynast_test1_expected_aln = Alignment.from_fasta_records(
parse_fasta(pynast_test1_expected_alignment), DNA)
self.pynast_test1_expected_fail = SequenceCollection.from_fasta_records(
parse_fasta(pynast_test1_expected_failure), DNA)