def bioseq_to_bwa_seq(self):
nseq = 100
for fmt in "fastq-sanger", "fastq-illumina", "fastq-solexa":
qkey = "solexa_quality" if fmt == "fastq-solexa" else "phred_quality"
for unknown in False, True:
g = u.random_reads_generator(nseq, fmt=fmt, unknown=unknown)
for i, (seq, q) in enumerate(g):
name = "foo-%d" % i
seq_str = "".join(seq)
bioseq = SeqRecord(Seq(seq_str, single_letter_alphabet),
id=name, name=name, description=name)
bioseq.letter_annotations[qkey] = q
n, m = len(bioseq), len(bioseq.name)
bwseq = bwa.alloc_seq(1, n, m)[0]
bwa.bioseq_to_bwa_seq(bioseq, bwseq, n, m, fmt)
self.assertEqual(bioseq.name, bwseq.get_name())
self.assertEqual(bioseq.seq.data[::-1], bwseq.get_seq())
self.assertEqual(reverse_complement(bioseq.seq.data),
bwseq.get_rseq())
# check that quality has been converted to sanger
if fmt == "fastq-solexa":
exp_q = [int(round(x+10*math.log10(1+10**(-x/10.)))) for x in q]
else:
exp_q = q
exp_qstr = "".join(chr(x+sg.Q_OFFSET["fastq-sanger"]) for x in exp_q)
self.assertEqual(bwseq.get_qual(), exp_qstr)
def bioseq_to_bwa_seq(self):
nseq = 100
for fmt in "fastq-sanger", "fastq-illumina", "fastq-solexa":
qkey = "solexa_quality" if fmt == "fastq-solexa" else "phred_quality"
for unknown in False, True:
g = u.random_reads_generator(nseq, fmt=fmt, unknown=unknown)
for i, (seq, q) in enumerate(g):
name = "foo-%d" % i
seq_str = "".join(seq)
bioseq = SeqRecord(Seq(seq_str, single_letter_alphabet),
id=name,
name=name,
description=name)
bioseq.letter_annotations[qkey] = q
n, m = len(bioseq), len(bioseq.name)
bwseq = bwa.alloc_seq(1, n, m)[0]
bwa.bioseq_to_bwa_seq(bioseq, bwseq, n, m, fmt)
self.assertEqual(bioseq.name, bwseq.get_name())
self.assertEqual(bioseq.seq.data[::-1], bwseq.get_seq())
self.assertEqual(reverse_complement(bioseq.seq.data),
bwseq.get_rseq())
# check that quality has been converted to sanger
if fmt == "fastq-solexa":
exp_q = [
int(round(x + 10 * math.log10(1 + 10**(-x / 10.))))
for x in q
]
else:
exp_q = q
exp_qstr = "".join(
chr(x + sg.Q_OFFSET["fastq-sanger"]) for x in exp_q)
self.assertEqual(bwseq.get_qual(), exp_qstr)
def build_bws_array(self):
# FIXME: plenty of UGLY code
nseq = 100
for fmt in "fastq-sanger", "fastq-illumina", "fastq-solexa":
qkey = "solexa_quality" if fmt == "fastq-solexa" else "phred_quality"
for unknown in False, True:
g = u.random_reads_generator(nseq,
fmt=fmt,
unknown=unknown,
pe=True)
bioseq_pairs, qseq_pairs = [], []
for i, read_pair in enumerate(g):
base_name = "foo-%d" % i
names = ["%s/%d" % (base_name, j) for j in 1, 2]
seq_strings = ["".join(read_pair[j][0]) for j in 0, 1]
q_strings = [
"".join(
chr(x + sg.Q_OFFSET[fmt]) for x in read_pair[j][1])
for j in 0, 1
]
bioseq_p = [
SeqRecord(Seq(seq_strings[j], single_letter_alphabet),
id=names[j],
name=names[j],
description=names[j]) for j in 0, 1
]
for j in 0, 1:
bioseq_p[j].letter_annotations[qkey] = read_pair[j][1]
bioseq_pairs.append(bioseq_p)
qseq_pairs.append([base_name])
for j in 0, 1:
for l in seq_strings, q_strings:
qseq_pairs[-1].append(l[j])
n = len(bioseq_pairs[0][0])
assert len(qseq_pairs[0][1]) == n
for src in "bioseq", "qseq":
seq_pairs = bioseq_pairs if src == "bioseq" else qseq_pairs
bwsa = bwa.build_bws_array(seq_pairs, qtype=fmt, src=src)
for j in 0, 1:
self.assertTrue(type(bwsa[j]) is bwa.bwa_seq_p_t)
for i in xrange(nseq):
bwseq = bwsa[j][i]
self.assertEqual(bwseq.len, n)
if src == "bioseq":
exp_name = bioseq_pairs[i][0].name
else:
exp_name = "%s/%d" % (qseq_pairs[i][0],
(j + 1))
self.assertEqual(len(bwseq.get_name()),
len(exp_name))
def build_bws_array(self):
# FIXME: plenty of UGLY code
nseq = 100
for fmt in "fastq-sanger", "fastq-illumina", "fastq-solexa":
qkey = "solexa_quality" if fmt == "fastq-solexa" else "phred_quality"
for unknown in False, True:
g = u.random_reads_generator(nseq, fmt=fmt, unknown=unknown, pe=True)
bioseq_pairs, qseq_pairs = [], []
for i, read_pair in enumerate(g):
base_name = "foo-%d" % i
names = ["%s/%d" % (base_name, j) for j in 1, 2]
seq_strings = ["".join(read_pair[j][0]) for j in 0, 1]
q_strings = ["".join(chr(x+sg.Q_OFFSET[fmt]) for x in read_pair[j][1])
for j in 0, 1]
bioseq_p = [SeqRecord(Seq(seq_strings[j], single_letter_alphabet),
id=names[j],
name=names[j],
description=names[j]) for j in 0, 1]
for j in 0, 1:
bioseq_p[j].letter_annotations[qkey] = read_pair[j][1]
bioseq_pairs.append(bioseq_p)
qseq_pairs.append([base_name])
for j in 0, 1:
for l in seq_strings, q_strings:
qseq_pairs[-1].append(l[j])
n = len(bioseq_pairs[0][0])
assert len(qseq_pairs[0][1]) == n
for src in "bioseq", "qseq":
seq_pairs = bioseq_pairs if src == "bioseq" else qseq_pairs
bwsa = bwa.build_bws_array(seq_pairs, qtype=fmt, src=src)
for j in 0, 1:
self.assertTrue(type(bwsa[j]) is bwa.bwa_seq_p_t)
for i in xrange(nseq):
bwseq = bwsa[j][i]
self.assertEqual(bwseq.len, n)
if src == "bioseq":
exp_name = bioseq_pairs[i][0].name
else:
exp_name = "%s/%d" % (qseq_pairs[i][0], (j+1))
self.assertEqual(len(bwseq.get_name()), len(exp_name))
