def test02(self):
"""
No output name, don't clean up
"""
q, t = self.data('two.fasta'), self.data('ten.fasta')
with sequtils.run_ssearch(q, t, cleanup=False) as aligns:
parsed = sequtils.parse_ssearch36(aligns)
self.assertEqual(set(['H59735', 'T70875']),
{d['q_name'] for d in parsed})
# should still exist since we specified 'cleanup=False'
self.assertTrue(path.exists(aligns.name))
def test03(self):
"""
No output name, clean up
"""
q, t = self.data('two.fasta'), self.data('ten.fasta')
with sequtils.run_ssearch(q, t) as aligns:
parsed = sequtils.parse_ssearch36(aligns)
self.assertEqual(set(['H59735', 'T70875']),
{d['q_name'] for d in parsed})
# should not still exist
self.assertFalse(path.exists(aligns.name))
def test01(self):
"""
Provide an output name
"""
q, t = self.data('two.fasta'), self.data('ten.fasta')
out = path.join(self.mkoutdir(), 'aligns.ssearch')
with sequtils.run_ssearch(q, t, out) as aligns:
self.assertEqual(out, aligns.name)
parsed = sequtils.parse_ssearch36(aligns)
self.assertEqual(set(['H59735', 'T70875']),
{d['q_name'] for d in parsed})
# should still exist since we provided a name for the output
self.assertTrue(path.exists(out))