def test_parse_m9_blast(self):
"""Parse blast output as expected"""
fna_6_hits = [M9(query='4502804.3.fna_6', subject='28_interest.fna',
percent_id=100.00, aln_length=14, mismatches=0,
gapopenings=0, q_start=42, q_end=55, s_start=98,
s_end=111, evalue=0.006, bitscore=28.2)]
fna_8_hits = [M9(query='4502804.3.fna_8',
subject='20_interest_hita.fna', percent_id=100.00,
aln_length=13, mismatches=0, gapopenings=0,
q_start=19, q_end=31, s_start=529, s_end=541,
evalue=0.059, bitscore=26.3),
M9(query='4502804.3.fna_8',
subject='20_interest_hitb.fna', percent_id=100.00,
aln_length=13, mismatches=0, gapopenings=0,
q_start=19, q_end=31, s_start=529, s_end=541,
evalue=0.059, bitscore=26.3),
M9(query='4502804.3.fna_8',
subject='20_interest_hitc.fna', percent_id=100.00,
aln_length=13, mismatches=0, gapopenings=0,
q_start=19, q_end=31, s_start=529, s_end=541,
evalue=0.059, bitscore=26.3)]
fna_9_hits = [M9(query='4502804.3.fna_9', subject='26_interest.fna',
percent_id=100.00, aln_length=14, mismatches=0,
gapopenings=0, q_start=114, q_end=127, s_start=3039,
s_end=3026, evalue=0.020, bitscore=28.2)]
exp = [(None, [copy(self.m9_empty)]),
('4502804.3.fna_6', fna_6_hits),
(None, [copy(self.m9_empty)]),
('4502804.3.fna_8', fna_8_hits),
('4502804.3.fna_9', fna_9_hits),
(None, [copy(self.m9_empty)])]
obs = parse_m9(self.blasttest)
self.assertEqual(obs, exp)
def test_parse_m9_sortmerna(self):
"""Parse sortmerna output as expected"""
fna_161_hits = [M9(query='QiimeExactMatch.4502806.3.fna_161',
subject='NZ_CAAQ01005666|642979345',
percent_id=87.8, aln_length=188, mismatches=23,
gapopenings=0, q_start=3, q_end=190, s_start=360,
s_end=547, evalue=1.05e-59, bitscore=234)]
fna_282_hits = [M9(query='QiimeExactMatch.4502806.3.fna_282',
subject='NZ_CAAX01000347|642979348',
percent_id=75, aln_length=164, mismatches=41,
gapopenings=0, q_start=3, q_end=166, s_start=1745,
s_end=1908, evalue=1.19e-22, bitscore=111)]
fna_504_hits = [M9(query='QiimeExactMatch.4502806.3.fna_504',
subject='NZ_CAAX01000347|642979348',
percent_id=96.4, aln_length=28, mismatches=1,
gapopenings=0, q_start=170, q_end=197, s_start=2575,
s_end=2602, evalue=0.00257, bitscore=47)]
fna_562_hits = [M9(query='QiimeExactMatch.4502806.3.fna_562',
subject='NZ_CAAQ01004522|642979345_hit_a',
percent_id=91.6, aln_length=143, mismatches=12,
gapopenings=0, q_start=3, q_end=145, s_start=1369,
s_end=1511, evalue=2.63e-50, bitscore=203.0),
M9(query='QiimeExactMatch.4502806.3.fna_562',
subject='NZ_CAAQ01004522|642979345_hit_b',
percent_id=91.6, aln_length=143, mismatches=12,
gapopenings=0, q_start=4, q_end=145, s_start=1369,
s_end=1511, evalue=2.63e-50, bitscore=203.0)]
fna_828_hits = [M9(query='QiimeExactMatch.4502806.3.fna_828',
subject='NZ_CAAU01001667|642979341',
percent_id=76, aln_length=122, mismatches=23,
gapopenings=7, q_start=10, q_end=131, s_start=88,
s_end=208, evalue=1.03e-12, bitscore=78.0)]
exp = [('QiimeExactMatch.4502806.3.fna_161', fna_161_hits),
('QiimeExactMatch.4502806.3.fna_282', fna_282_hits),
('QiimeExactMatch.4502806.3.fna_504', fna_504_hits),
('QiimeExactMatch.4502806.3.fna_562', fna_562_hits),
('QiimeExactMatch.4502806.3.fna_828', fna_828_hits)]
obs = parse_m9(self.smrtest)
self.assertEqual(obs, exp)
def test_parse_m9_bad(self):
"""Raise on an incomplete record"""
with self.assertRaises(ValueError):
parse_m9(self.smrtest_bad)