def test_blast_genome(self):
"""blast_genome should return raw BLAST output."""
formatdb_cmd = 'formatdb -p F -o T -i %s' % self.subjectdb_fp
system(formatdb_cmd)
self._paths_to_clean_up.append("formatdb.log")
for suffix in ["nhr", "nin", "nsd", "nsi", "nsq"]:
self._paths_to_clean_up.append(".".join(
[self.subjectdb_fp, suffix]))
raw_output = blast_genome(TEST_BLAST_DB_LINES,
self.subjectdb_fp,
e_value=1e-4,
max_hits=100,
word_size=28,
working_dir="./",
blast_mat_root=None)
i = 0
for line in raw_output:
if line.startswith("#"):
i += 1
continue # comments depend on tmpfilename, BLAST version
self.assertEqual(raw_output[i], EXP_BLAST_OUTPUT[i])
i += 1
def test_blast_genome(self):
"""blast_genome should return raw BLAST output."""
formatdb_cmd = 'formatdb -p F -o T -i %s' % self.subjectdb_fp
system(formatdb_cmd)
self._paths_to_clean_up.append("formatdb.log")
for suffix in ["nhr", "nin", "nsd", "nsi", "nsq"]:
self._paths_to_clean_up.append(".".join(
[self.subjectdb_fp, suffix]))
raw_output = blast_genome(TEST_BLAST_DB_LINES, self.subjectdb_fp,
e_value=1e-4, max_hits=100, word_size=28,
working_dir="./", blast_mat_root=None)
i = 0
for line in raw_output:
if line.startswith("#"):
i += 1
continue # comments depend on tmpfilename, BLAST version
self.assertEqual(raw_output[i], EXP_BLAST_OUTPUT[i])
i += 1