def setUp(self):
self.toy_data = [
["name1", "CAAAT", "latte", "CAGAT", "acqua"],
["name2", "TTAGG", "beefy", "CTTGG", "caffe"],
]
self.toy_bwsa = bwa.build_bws_array(self.toy_data,
qtype="fastq-illumina")
def test_build_bws_array_with_trim_qual_zero(self):
pair = ( # read, qual, trimmed length at qual=15
("pair1",
"ATNCACCTGCCTTGGCCTCGCAAAGTGCTGGGATTACAGGCATGANNNNNNNNNNNNNNNNNNCNGTNNNNNNNNNNNNNTNCANATNNNNNNNNNNNTG",
"==#@7::;;?FF?FFGGGFFGGGGE=CDEAE=AE?BBC??@###########################################################",
"TTATAAGCACTGCACATAACTTTCTCCCTAATCTTTACAACAATCNNNTNNNCNNANNNNNCNCAGGNNNNCNNGNNNNNGNCANTGNNNNNNNNNNNGT",
"EFDFFEEC?BEEAEE=A?CCE??EEAEEEEEECECEDEAC5@;7?#######################################################"
), )
bwsa = bwa.build_bws_array(pair, qtype="fastq-sanger", trim_qual=0)
self.assertEqual(100, bwsa[0][0].clip_len)
self.assertEqual(100, bwsa[1][0].clip_len)
for seq_array in bwsa:
bwa.free_seq(len(pair), seq_array)
def test_build_bws_array_with_illumina_q(self):
pair = (
("pair1",
"GCGTTAGTTTGTGGTGAAAGAAGCAAAATATTATGAATTTTGAAAATCTAGAGTCAATCTTCAAATTTCTTTTTATTCATTAATATCTCTGGCCTTTGTT",
"TcLacaU_b_a\\aa`L\\a]X`dddYM^Z\\W]]W]WWbbYTZLZLZRI[VYQVWUU^b\\ccTc\\c^cYcYcZ^_ULUVUX[bY`^BBBBBBBBBBBBBBBB",
"ATCAATCTAGGAGTTTGTATATACCACAAGAACAATGCTTGTCAAATCACTCACTTCTTTTCCCCTCTCTGGAGCCAGGCTTCGAGAAGTTGTATCCAGA",
"B_a`aaTT__Q\\UQV^Z```\\VRKYQHUVIRLQQTTK]`^Z]]Y]_Y_Yb`da`^`aaac]eKdddfdefefecffffdaffffffefdedcffdeffff"),
)
lengths = (85,100)
bwsa = bwa.build_bws_array(pair, qtype="fastq-illumina", trim_qual=15)
self.assertEqual(lengths[0], bwsa[0][0].clip_len)
self.assertEqual(lengths[1], bwsa[1][0].clip_len)
for seq_array in bwsa:
bwa.free_seq(len(pair), seq_array)
def test_build_bws_array_with_trim_qual_zero(self):
pair = ( # read, qual, trimmed length at qual=15
("pair1",
"ATNCACCTGCCTTGGCCTCGCAAAGTGCTGGGATTACAGGCATGANNNNNNNNNNNNNNNNNNCNGTNNNNNNNNNNNNNTNCANATNNNNNNNNNNNTG",
"==#@7::;;?FF?FFGGGFFGGGGE=CDEAE=AE?BBC??@###########################################################",
"TTATAAGCACTGCACATAACTTTCTCCCTAATCTTTACAACAATCNNNTNNNCNNANNNNNCNCAGGNNNNCNNGNNNNNGNCANTGNNNNNNNNNNNGT",
"EFDFFEEC?BEEAEE=A?CCE??EEAEEEEEECECEDEAC5@;7?#######################################################"
),
)
bwsa = bwa.build_bws_array(pair, qtype="fastq-sanger", trim_qual=0)
self.assertEqual(100, bwsa[0][0].clip_len)
self.assertEqual(100, bwsa[1][0].clip_len)
for seq_array in bwsa:
bwa.free_seq(len(pair), seq_array)
def test_build_bws_array_with_illumina_q(self):
pair = ((
"pair1",
"GCGTTAGTTTGTGGTGAAAGAAGCAAAATATTATGAATTTTGAAAATCTAGAGTCAATCTTCAAATTTCTTTTTATTCATTAATATCTCTGGCCTTTGTT",
"TcLacaU_b_a\\aa`L\\a]X`dddYM^Z\\W]]W]WWbbYTZLZLZRI[VYQVWUU^b\\ccTc\\c^cYcYcZ^_ULUVUX[bY`^BBBBBBBBBBBBBBBB",
"ATCAATCTAGGAGTTTGTATATACCACAAGAACAATGCTTGTCAAATCACTCACTTCTTTTCCCCTCTCTGGAGCCAGGCTTCGAGAAGTTGTATCCAGA",
"B_a`aaTT__Q\\UQV^Z```\\VRKYQHUVIRLQQTTK]`^Z]]Y]_Y_Yb`da`^`aaac]eKdddfdefefecffffdaffffffefdedcffdeffff"
), )
lengths = (85, 100)
bwsa = bwa.build_bws_array(pair, qtype="fastq-illumina", trim_qual=15)
self.assertEqual(lengths[0], bwsa[0][0].clip_len)
self.assertEqual(lengths[1], bwsa[1][0].clip_len)
for seq_array in bwsa:
bwa.free_seq(len(pair), seq_array)
def test_build_bws_array_without_qual_str(self):
# make tuples substituting None for the quality strings in toy_data
toy = map(lambda t: (t[0], t[1], None, t[3], None), self.toy_data)
bwsa = bwa.build_bws_array(toy)
for i in xrange(len(self.toy_data)):
# verify name, sequence (which is reversed)
self.assertEqual(self.toy_data[i][0], bwsa[0][i].get_name())
self.assertEqual(self.toy_data[i][0], bwsa[1][i].get_name())
self.assertEqual(self.toy_data[i][1], bwsa[0][i].get_seq()[::-1])
self.assertEqual(self.toy_data[i][3], bwsa[1][i].get_seq()[::-1])
# ensure that the returned quality string is empty
self.assertEqual('', bwsa[0][i].get_qual_string())
self.assertEqual('', bwsa[1][i].get_qual_string())
for seq_array in bwsa:
bwa.free_seq(len(toy), seq_array)
def test_build_bws_array_without_qual_str(self):
# make tuples substituting None for the quality strings in toy_data
toy = map(lambda t: (t[0], t[1], None, t[3], None), self.toy_data)
bwsa = bwa.build_bws_array(toy)
for i in xrange(len(self.toy_data)):
# verify name, sequence (which is reversed)
self.assertEqual(self.toy_data[i][0], bwsa[0][i].get_name())
self.assertEqual(self.toy_data[i][0], bwsa[1][i].get_name())
self.assertEqual(self.toy_data[i][1], bwsa[0][i].get_seq()[::-1])
self.assertEqual(self.toy_data[i][3], bwsa[1][i].get_seq()[::-1])
# ensure that the returned quality string is empty
self.assertEqual('', bwsa[0][i].get_qual_string())
self.assertEqual('', bwsa[1][i].get_qual_string())
for seq_array in bwsa:
bwa.free_seq(len(toy), seq_array)
def test_trimming_min_length(self):
pair = ( # (name, r1, q1, r2, q2)
("seq_name",
"NNNNNNNNNNNNACAGCTTTTGAGNGGGGCNCAGCCTCTTCCTTGTGGTGTTGCAGGACGGCAGGGAGTCAGTTGGGTTTCNACTCTTTAAGGACAGTGA",
"####################################################################################################",
"TTTTTATTTCTAGTGTTTATATTGATGAACAGAAATATACTGACATATTAACTTTTTTCATATAAATTTTTTCAAATTTTTGGTTAAGGCTTTTTCTGTC",
"GGGGGF@EGGD;EEEGG??EDEEDAE==E?EEE??>B6C:=CDCBGFGFFFGFGGF=EF5<?=)=9B6?BAA-A:;;>;5*2*57AA>AA>AA>CA@CED"),
)
# The first sequence should have a clipped length of 35 at q=15.
# 35 is the minimum trimmed sequence length.
bwsa = bwa.build_bws_array(pair, qtype="fastq-sanger", trim_qual=15)
self.assertEqual(100, bwsa[0][0].full_len)
self.assertEqual(35, bwsa[0][0].clip_len)
self.assertEqual(35, bwsa[0][0].len)
self.assertEqual(100, bwsa[1][0].clip_len) # this one isn't clipped at q=15
for seq_array in bwsa:
bwa.free_seq(len(pair), seq_array)
def test_trimming_min_length(self):
pair = ( # (name, r1, q1, r2, q2)
("seq_name",
"NNNNNNNNNNNNACAGCTTTTGAGNGGGGCNCAGCCTCTTCCTTGTGGTGTTGCAGGACGGCAGGGAGTCAGTTGGGTTTCNACTCTTTAAGGACAGTGA",
"####################################################################################################",
"TTTTTATTTCTAGTGTTTATATTGATGAACAGAAATATACTGACATATTAACTTTTTTCATATAAATTTTTTCAAATTTTTGGTTAAGGCTTTTTCTGTC",
"GGGGGF@EGGD;EEEGG??EDEEDAE==E?EEE??>B6C:=CDCBGFGFFFGFGGF=EF5<?=)=9B6?BAA-A:;;>;5*2*57AA>AA>AA>CA@CED"
), )
# The first sequence should have a clipped length of 35 at q=15.
# 35 is the minimum trimmed sequence length.
bwsa = bwa.build_bws_array(pair, qtype="fastq-sanger", trim_qual=15)
self.assertEqual(100, bwsa[0][0].full_len)
self.assertEqual(35, bwsa[0][0].clip_len)
self.assertEqual(35, bwsa[0][0].len)
self.assertEqual(100,
bwsa[1][0].clip_len) # this one isn't clipped at q=15
for seq_array in bwsa:
bwa.free_seq(len(pair), seq_array)
def setUp(self): self.toy_data = [ [ "name1", "CAAAT", "latte", "CAGAT", "acqua" ], [ "name2", "TTAGG", "beefy", "CTTGG", "caffe" ], ] self.toy_bwsa = bwa.build_bws_array(self.toy_data, qtype="fastq-illumina")
