def test_predict_crispr(self):
for fp, params, flags in zip(self.positive_fps, self.positive_params,
self.positive_flags):
prefix = self.positive_prefix
res = predict_crispr(fp, self.temp_dir,
prefix,
gff=flags['gff'],
gffFull=flags['gffFull'],
spac=flags['spacers'], params=params)
self.assertEqual(res['ExitStatus'], 0)
if flags['gff']:
suffix = 'gff'
elif flags['gffFull']:
suffix = 'gffFull'
else:
suffix = 'crisprs'
fp = self.get_minced_path('.'.join([prefix, suffix]))
with open(fp) as f:
self.assertEqual(
# skip comment lines as some contain runtime info
[i for i in f.readlines()
if not i.startswith('Time')],
[j for j in res['output'].readlines()
if not j.startswith('Time')])
# SPACERS flag produces an *additional* OUT_spacers.fa file
# other flags produce OUT.FLAG outputs
if flags['spacers']:
suffix = 'spacers.fa'
fp = self.get_minced_path('_'.join([prefix, suffix]))
with open(fp) as f:
self.assertEqual(f.read(), res['spacers'].read())
res['StdOut'].close()
res['StdErr'].close()
def test_predict_crispr_wrong_input(self):
for fp in self.negative_fps:
with self.assertRaisesRegex(
ApplicationError,
r'Error constructing CommandLineAppResult.'):
predict_crispr(fp, self.temp_dir, 'foo')