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_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_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)