def _filtered_fastq_generator(fw_fastq_handler, rv_fastq_handler, min_len,
max_len, retain_len, counters):
paired_fastq_records = paired_fastq_generator(fw_fastq_handler,
rv_fastq_handler, True)
for curr_pair_fastq_records in paired_fastq_records:
counters["num_pairs"] += 1
_report_progress(counters["num_pairs"])
fw_record = curr_pair_fastq_records[0]
fw_passing_seq = _check_and_trim_seq(_get_upper_seq(fw_record),
min_len, max_len, retain_len,
False)
if fw_passing_seq is not None:
rv_record = curr_pair_fastq_records[1]
rv_passing_seq = _check_and_trim_seq(_get_upper_seq(rv_record),
min_len, max_len, retain_len,
True)
if rv_passing_seq is not None:
counters["num_pairs_passing"] += 1
fw_record.sequence = fw_passing_seq
fw_record.quality = trim_seq(fw_record.quality, retain_len,
False)
rv_record.sequence = rv_passing_seq
rv_record.quality = trim_seq(rv_record.quality, retain_len,
True)
yield fw_record, rv_record
def test_trim_seq_short(self):
input_seq = "ACGT"
retain_len = 5
# trim from 5p end
with self.assertRaises(ValueError):
trim_seq(input_seq, retain_len, False)
# trim from 3p end
with self.assertRaises(ValueError):
trim_seq(input_seq, retain_len, True)
def test_trim_seq_exact(self):
input_seq = "ACGT"
retain_len = 4
# trim from 5p end
output_5p = trim_seq(input_seq, retain_len, False)
self.assertEqual(input_seq, output_5p)
# trim from 3p end
output_3p = trim_seq(input_seq, retain_len, True)
self.assertEqual(input_seq, output_3p)
def test_trim_seq_long(self):
input_seq = "ACGT"
retain_len = 3
# trim from 5p end
output_5p = trim_seq(input_seq, retain_len, False)
self.assertEqual("CGT", output_5p)
# trim from 3p end
output_3p = trim_seq(input_seq, retain_len, True)
self.assertEqual("ACG", output_3p)
def _check_and_trim_seq(input_seq, min_len, max_len, retain_len,
retain_5p_end):
result = None
seq_len = len(input_seq)
if seq_len >= min_len and seq_len <= max_len:
result = trim_seq(input_seq, retain_len, retain_5p_end)
return result
def trim_grnas(grnas_name_and_seq_list, retain_len):
result = []
for name_seq_tuple in grnas_name_and_seq_list:
grna_name = name_seq_tuple[0]
full_seq = name_seq_tuple[1]
trimmed_seq = trim_seq(full_seq, retain_len, False) # False = do not retain from 5p end but from 3p end
result.append((grna_name, trimmed_seq))
return result
def _filtered_fastq_generator(fw_fastq_handler, rv_fastq_handler, min_len, max_len, retain_len, counters):
paired_fastq_records = paired_fastq_generator(fw_fastq_handler, rv_fastq_handler, True)
for curr_pair_fastq_records in paired_fastq_records:
counters["num_pairs"] += 1
_report_progress(counters["num_pairs"])
fw_record = curr_pair_fastq_records[0]
fw_passing_seq = _check_and_trim_seq(_get_upper_seq(fw_record), min_len, max_len, retain_len, False)
if fw_passing_seq is not None:
rv_record = curr_pair_fastq_records[1]
rv_passing_seq = _check_and_trim_seq(_get_upper_seq(rv_record), min_len, max_len, retain_len, True)
if rv_passing_seq is not None:
counters["num_pairs_passing"] += 1
fw_record.sequence = fw_passing_seq
fw_record.quality = trim_seq(fw_record.quality, retain_len, False)
rv_record.sequence = rv_passing_seq
rv_record.quality = trim_seq(rv_record.quality, retain_len, True)
yield fw_record, rv_record
def trim_grnas(grnas_name_and_seq_list, retain_len):
result = []
for name_seq_tuple in grnas_name_and_seq_list:
grna_name = name_seq_tuple[0]
full_seq = name_seq_tuple[1]
trimmed_seq = trim_seq(
full_seq, retain_len,
False) # False = do not retain from 5p end but from 3p end
result.append((grna_name, trimmed_seq))
return result
def _check_and_trim_seq(input_seq, min_len, max_len, retain_len, retain_5p_end):
result = None
seq_len = len(input_seq)
if seq_len >= min_len and seq_len <= max_len:
result = trim_seq(input_seq, retain_len, retain_5p_end)
return result