def test_blastx_parser(self):
"Testing blastx parser"
blastx_output = open(testutil.datafile("blastx_output.txt"), "r")
seq_dict = {"gi|171854975|dbj|AB364477.1|": self.dna["gi|171854975|dbj|AB364477.1|"]}
try:
results = blast.read_blast_alignment(
blastx_output, seq_dict, blast.BlastIDIndex(self.prot), translateSrc=True
)
finally:
blastx_output.close()
correct = [
(143, 143, 429, 0.53146853146853146),
(143, 145, 429, 0.28275862068965518),
(143, 145, 429, 0.28965517241379313),
(143, 145, 429, 0.29655172413793102),
(143, 145, 429, 0.30344827586206896),
(144, 144, 432, 0.4513888888888889),
(144, 144, 432, 0.4513888888888889),
(145, 145, 435, 0.45517241379310347),
(145, 145, 435, 0.51034482758620692),
(146, 142, 438, 0.35616438356164382),
(146, 146, 438, 0.4589041095890411),
(146, 146, 438, 0.46575342465753422),
(146, 146, 438, 0.4726027397260274),
(146, 146, 438, 0.4726027397260274),
(146, 146, 438, 0.4863013698630137),
(146, 146, 438, 0.59589041095890416),
(146, 146, 438, 0.62328767123287676),
(146, 146, 438, 0.66438356164383561),
(146, 146, 438, 0.74657534246575341),
(146, 146, 438, 0.91095890410958902),
(146, 146, 438, 0.97945205479452058),
]
check_results([results], correct, lambda t: (len(t[0]), len(t[1]), len(t[0].sequence), t[2].pIdentity()))
def test_multiblast_parser_long(self):
"Testing multiblast parser with long input"
longerFile = testutil.datafile("sp_all_hbb")
sp_all_hbb = seqdb.SequenceFileDB(longerFile)
filename = testutil.datafile("multiblast_long_output.txt")
multiblast_output = open(filename, "r")
try:
al = cnestedlist.NLMSA("blasthits", "memory", pairwiseMode=True, bidirectional=False)
al = blast.read_blast_alignment(multiblast_output, sp_all_hbb, self.prot, al)
finally:
multiblast_output.close()
al.build()
results = []
for seq in sp_all_hbb.values():
try:
results.append(al[seq])
except KeyError:
pass
correctfile = file(testutil.datafile("multiblast_long_correct.txt"), "r")
try:
correct = []
for line in correctfile:
t = line.split()
correct.append((t[0], t[1], float(t[2])))
finally:
correctfile.close()
check_results(results, correct, pair_identity_tuple)
def test_multiblast_parser(self):
"Testing multiblast parser"
multiblast_output = open(testutil.datafile("multiblast_output.txt"), "r")
try:
al = cnestedlist.NLMSA("blasthits", "memory", pairwiseMode=True, bidirectional=False)
al = blast.read_blast_alignment(multiblast_output, self.prot, blast.BlastIDIndex(self.prot), al)
finally:
multiblast_output.close()
al.build()
results = [al[seq] for seq in self.prot.values()]
check_results(results, correct_multiblast_results, pair_identity_tuple)
def test_blastp_parser(self):
"Testing blastp parser"
blastp_output = open(testutil.datafile("blastp_output.txt"), "r")
seq_dict = {"HBB1_XENLA": self.prot["HBB1_XENLA"]}
prot_index = blast.BlastIDIndex(self.prot)
try:
alignment = blast.read_blast_alignment(blastp_output, seq_dict, prot_index)
results = alignment[self.prot["HBB1_XENLA"]]
finally:
blastp_output.close()
check_results([results], blastp_correct_results, pair_identity_tuple)
def test_tblastn_parser(self):
"Testing tblastn parser"
seq_dict = {"HBB1_XENLA": self.prot["HBB1_XENLA"]}
dna_db = blast.BlastIDIndex(self.dna)
tblastn_output = open(testutil.datafile("tblastn_output.txt"), "r")
try:
al = blast.read_blast_alignment(tblastn_output, seq_dict, dna_db, translateDest=True)
result = al[self.prot["HBB1_XENLA"]]
finally:
tblastn_output.close()
src, dest, edge = iter(result.edges()).next()
self.assertEqual(
str(src),
"LTAHDRQLINSTWGKLCAKTIGQEALGRLLWTYPWTQRYFSSFGNLNSADAVFHNEAVAAHGEK"
"VVTSIGEAIKHMDDIKGYYAQLSKYHSETLHVDPLNFKRFGGCLSIALARHFHEEYTPELHAAY"
"EHLFDAIADALGKGYH",
)
self.assertEqual(
str(dest),
"LTDAEKAAVSGLWGKVNSDEVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNAKVKAHGKK"
"VITAFNEGLNHLDSLKGTFASLSELHCDKLHVDPENFRLLGNMIVIVLGHHLGKDFTPAAQAAF"
"QKVMAGVATALAHKYH",
)
self.assertEqual(
str(dest.sequence),
"CTGACTGATGCTGAGAAGGCTGCTGTCTCTGGCCTGTGGGGAAAGGTGAACTCCGATGAAGTTG"
"GTGGTGAGGCCCTGGGCAGGCTGCTGGTTGTCTACCCTTGGACCCAGAGGTACTTTGATAGCTT"
"TGGAGACCTATCCTCTGCCTCTGCTATCATGGGTAATGCCAAAGTGAAGGCCCATGGCAAGAAA"
"GTGATAACTGCCTTTAACGAGGGCCTGAATCACTTGGACAGCCTCAAGGGCACCTTTGCCAGCC"
"TCAGTGAGCTCCACTGTGACAAGCTCCATGTGGATCCTGAGAACTTCAGGCTCCTGGGCAATAT"
"GATCGTGATTGTGCTGGGCCACCACCTGGGCAAGGATTTCACCCCCGCTGCACAGGCTGCCTTC"
"CAGAAGGTGATGGCTGGAGTGGCCACTGCCCTGGCTCACAAGTACCAC",
)
self.assertAlmostEqual(edge.pIdentity(), 0.451, 3)