def test_cmscan_fasta(self):
params = {'--rfam': None, '--noali': None}
for f in self.positive_fps:
res = cmscan_fasta(self.cm_fp, f, self.temp_fp, 0.1, 1, params)
res['StdOut'].close()
res['StdErr'].close()
obs = res['--tblout']
out_fp = '.'.join([f, 'tblout'])
with open(out_fp) as exp:
# skip comment lines as some contain running time info
self.assertListEqual(
[i for i in exp.readlines() if not i.startswith('#')],
[j for j in obs.readlines() if not j.startswith('#')])
obs.close()
def test_cmscan_fasta(self):
params = {'--rfam': None, '--noali': None}
for f in self.positive_fps:
res = cmscan_fasta(self.cm_fp, f, self.temp_fp, 0.1, 1, params)
res['StdOut'].close()
res['StdErr'].close()
obs = res['--tblout']
out_fp = '.'.join([f, 'tblout'])
with open(out_fp) as exp:
# skip comment lines as some contain running time info
self.assertListEqual(
[i for i in exp.readlines() if not i.startswith('#')],
[j for j in obs.readlines() if not j.startswith('#')])
obs.close()
def test_cmscan_fasta_wrong_input(self):
for fp in self.negative_fps:
with self.assertRaisesRegex(
ApplicationError,
r'Error: Sequence file .* is empty or misformatted'):
cmscan_fasta(self.cm_fp, fp, 'foo')
def test_cmscan_fasta_wrong_input(self):
for fp in self.negative_fps:
with self.assertRaisesRegex(
ApplicationError,
r'Error: Sequence file .* is empty or misformatted'):
cmscan_fasta(self.cm_fp, fp, 'foo')