def test_bwa_init_sequences_no_trim(self):
row_type = (ct.c_char_p * 3)
pointers = (row_type * len(self.toy_data))()
q_offset = bwa.Q_OFFSET["fastq-illumina"]
for i, row in enumerate(self.toy_data):
for j in xrange(3):
pointers[i][j] = row[j]
array = bwa.init_sequences(ct.cast(pointers, bwa.p_char_p),
len(self.toy_data), q_offset, 0)
resulting_qoffset = q_offset - bwa.Q_OFFSET["fastq-sanger"]
for i, row in enumerate(self.toy_data):
self.assertEqual(-1, array[i].tid)
self.assertEqual(len(row[1]), array[i].len)
self.assertEqual(len(row[1]), array[i].full_len)
self.assertEqual(len(row[1]), array[i].clip_len)
self.assertEqual(row[0], array[i].get_name())
self.assertEqual(row[1][::-1], array[i].get_seq())
self.assertEqual(
row[2], ''.join([
chr(array[i].qual[k] + resulting_qoffset)
for k in xrange(array[i].full_len)
]))
bwa.free_seq(len(self.toy_data), array)
def test_init_sequences_with_trimming(self):
data = []
data.append(("seq1", "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN",
"####################################################################################################"))
row_type = (ct.c_char_p * 3)
pointers = (row_type*len(data))()
q_offset = bwa.Q_OFFSET["fastq-sanger"]
for i, row in enumerate(data):
for j in xrange(3):
pointers[i][j] = row[j]
array = bwa.init_sequences( ct.cast(pointers, bwa.p_char_p), len(data), q_offset, 15)
self.assertEqual(35, array[0].clip_len)
bwa.free_seq(len(data), 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_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_init_sequences_with_trimming(self):
data = []
data.append((
"seq1",
"NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN",
"####################################################################################################"
))
row_type = (ct.c_char_p * 3)
pointers = (row_type * len(data))()
q_offset = bwa.Q_OFFSET["fastq-sanger"]
for i, row in enumerate(data):
for j in xrange(3):
pointers[i][j] = row[j]
array = bwa.init_sequences(ct.cast(pointers, bwa.p_char_p), len(data),
q_offset, 15)
self.assertEqual(35, array[0].clip_len)
bwa.free_seq(len(data), 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_bwa_init_sequences_no_trim(self): row_type = (ct.c_char_p * 3) pointers = (row_type*len(self.toy_data))() q_offset = bwa.Q_OFFSET["fastq-illumina"] for i, row in enumerate(self.toy_data): for j in xrange(3): pointers[i][j] = row[j] array = bwa.init_sequences( ct.cast(pointers, bwa.p_char_p), len(self.toy_data), q_offset, 0) resulting_qoffset = q_offset - bwa.Q_OFFSET["fastq-sanger"] for i, row in enumerate(self.toy_data): self.assertEqual(-1, array[i].tid) self.assertEqual(len(row[1]), array[i].len) self.assertEqual(len(row[1]), array[i].full_len) self.assertEqual(len(row[1]), array[i].clip_len) self.assertEqual(row[0], array[i].get_name()) self.assertEqual(row[1][::-1], array[i].get_seq()) self.assertEqual(row[2], ''.join( [chr(array[i].qual[k]+resulting_qoffset) for k in xrange(array[i].full_len)] )) bwa.free_seq(len(self.toy_data), array)
def tearDown(self): for seq_array in self.toy_bwsa: bwa.free_seq(len(self.toy_data), seq_array)
def tearDown(self):
for seq_array in self.toy_bwsa:
bwa.free_seq(len(self.toy_data), seq_array)