def _process_roi(roi, samdata, amplicon_ref, reverse_comp=False):
roi_dict = {'region': roi.position_range}
range_match = re.search('(\d*)-(\d*)', roi.position_range)
if not range_match:
return roi_dict
start = int(range_match.group(1)) - 1
end = int(range_match.group(2))
aa_sequence_counter = Counter()
nt_sequence_counter = Counter()
depth = 0
for read in samdata.fetch(amplicon_ref, start, end):
rstart = read.reference_start
if rstart <= start:
nt_sequence = DNA(
read.query_alignment_sequence[start - rstart:end - rstart])
if reverse_comp:
nt_sequence = nt_sequence.reverse_complement()
#scikit-bio doesn't support translating degenerate bases currently, so we will just throw out reads with degenerates for now
if nt_sequence.has_degenerates():
continue
aa_sequence = nt_sequence.translate()
aa_string = str(aa_sequence).replace('*', 'x')
if aa_string:
nt_sequence_counter.update([str(nt_sequence)])
aa_sequence_counter.update([aa_string])
depth += 1
if len(aa_sequence_counter) == 0:
roi_dict['flag'] = "region not found"
return roi_dict
aa_consensus = aa_sequence_counter.most_common(1)[0][0]
nt_consensus = nt_sequence_counter.most_common(1)[0][0]
num_changes = 0
reference = roi.aa_sequence
consensus = aa_consensus
if roi.nt_sequence:
reference = roi.nt_sequence
consensus = nt_consensus
for i in range(len(reference)):
if len(consensus) <= i or reference[i] != consensus[i]:
num_changes += 1
roi_dict['most_common_aa_sequence'] = aa_consensus
roi_dict['most_common_nt_sequence'] = nt_consensus
roi_dict['reference'] = reference
roi_dict['changes'] = str(num_changes)
roi_dict['aa_sequence_distribution'] = aa_sequence_counter
roi_dict['nt_sequence_distribution'] = nt_sequence_counter
roi_dict['depth'] = str(depth)
return roi_dict
def _process_roi(roi, samdata, amplicon_ref, reverse_comp=False):
roi_dict = {'region':roi.position_range}
range_match = re.search('(\d*)-(\d*)', roi.position_range)
if not range_match:
return roi_dict
start = int(range_match.group(1)) - 1
end = int(range_match.group(2))
aa_sequence_counter = Counter()
nt_sequence_counter = Counter()
depth = 0
for read in samdata.fetch(amplicon_ref, start, end):
rstart = read.reference_start
if rstart <= start:
nt_sequence = DNA(read.query_alignment_sequence[start-rstart:end-rstart])
if reverse_comp:
nt_sequence = nt_sequence.reverse_complement()
#scikit-bio doesn't support translating degenerate bases currently, so we will just throw out reads with degenerates for now
if nt_sequence.has_degenerates():
continue
aa_sequence = nt_sequence.translate()
aa_string = str(aa_sequence).replace('*', 'x')
if aa_string:
nt_sequence_counter.update([str(nt_sequence)])
aa_sequence_counter.update([aa_string])
depth += 1
if len(aa_sequence_counter) == 0:
roi_dict['flag'] = "region not found"
return roi_dict
aa_consensus = aa_sequence_counter.most_common(1)[0][0]
nt_consensus = nt_sequence_counter.most_common(1)[0][0]
num_changes = 0
reference = roi.aa_sequence
consensus = aa_consensus
if roi.nt_sequence:
reference = roi.nt_sequence
consensus = nt_consensus
for i in range(len(reference)):
if len(consensus) <= i or reference[i] != consensus[i]:
num_changes += 1
roi_dict['most_common_aa_sequence'] = aa_consensus
roi_dict['most_common_nt_sequence'] = nt_consensus
roi_dict['reference'] = reference
roi_dict['changes'] = str(num_changes)
roi_dict['aa_sequence_distribution'] = aa_sequence_counter
roi_dict['nt_sequence_distribution'] = nt_sequence_counter
roi_dict['depth'] = str(depth)
return roi_dict
def _process_roi_SMOR(roi, samdata, amplicon_ref, reverse_comp=False):
from operator import attrgetter
roi_dict = {'region': roi.position_range}
range_match = re.search('(\d*)-(\d*)', roi.position_range)
if not range_match:
return roi_dict
start = int(range_match.group(1)) - 1
end = int(range_match.group(2))
expected_length = end - start
aa_sequence_counter = Counter()
nt_sequence_counter = Counter()
depth = 0
reads = iter(
sorted(samdata.fetch(amplicon_ref, start, end),
key=attrgetter('query_name')))
for read, pair in pairwise(reads):
if read.query_name != pair.query_name:
continue
rstart1 = read.reference_start
rstart2 = pair.reference_start
alignment_length1 = read.get_overlap(start, end)
alignment_length2 = pair.get_overlap(start, end)
#throw out reads that either have gaps in the ROI or don't cover the whole ROI
if alignment_length1 != expected_length or alignment_length2 != expected_length:
continue
if rstart1 <= start:
qend = qstart = None
for (qpos, rpos) in read.get_aligned_pairs():
if rpos == start:
qstart = qpos
if rpos == end:
qend = qpos
#throw out reads with insertions in the ROI
if not qend or not qstart or qend - qstart != expected_length:
continue
nt_sequence = DNA(read.query_alignment_sequence[qstart:qend])
if rstart2 <= start:
qend = qstart = None
for (qpos, rpos) in pair.get_aligned_pairs():
if rpos == start:
qstart = qpos
if rpos == end:
qend = qpos
#throw out reads with insertions in the ROI
if not qend or not qstart or qend - qstart != expected_length:
continue
nt_sequence2 = DNA(pair.query_alignment_sequence[qstart:qend])
if nt_sequence != nt_sequence2:
continue
else:
if reverse_comp:
nt_sequence = nt_sequence.reverse_complement()
#scikit-bio doesn't support translating degenerate bases currently, so we will just throw out reads with degenerates for now
if nt_sequence.has_degenerates():
continue
aa_sequence = nt_sequence.translate()
aa_string = str(aa_sequence).replace('*', 'x')
if aa_string:
nt_sequence_counter.update([str(nt_sequence)])
aa_sequence_counter.update([aa_string])
depth += 1
if len(aa_sequence_counter) == 0:
roi_dict['flag'] = "region not found"
return roi_dict
aa_consensus = aa_sequence_counter.most_common(1)[0][0]
nt_consensus = nt_sequence_counter.most_common(1)[0][0]
num_changes = 0
reference = roi.aa_sequence
consensus = aa_consensus
if roi.nt_sequence:
reference = roi.nt_sequence
consensus = nt_consensus
for i in range(len(reference)):
if len(consensus) <= i or reference[i] != consensus[i]:
num_changes += 1
roi_dict['most_common_aa_sequence'] = aa_consensus
roi_dict['most_common_nt_sequence'] = nt_consensus
roi_dict['reference'] = reference
roi_dict['changes'] = str(num_changes)
roi_dict['aa_sequence_distribution'] = aa_sequence_counter
roi_dict['nt_sequence_distribution'] = nt_sequence_counter
roi_dict['depth'] = str(depth)
return roi_dict
def _process_roi(roi, samdata, amplicon_ref, reverse_comp=False):
roi_dict = {'region': roi.position_range}
range_match = re.search('(\d*)-(\d*)', roi.position_range)
if not range_match:
return roi_dict
start = int(range_match.group(1)) - 1
end = int(range_match.group(2))
expected_length = end - start
aa_sequence_counter = Counter()
aa_sequence_counter_temp = Counter()
nt_sequence_counter = Counter()
depth = 0
significant = False
if not roi.aa_sequence:
roi.aa_sequence = str(DNA(roi.nt_sequence).translate()).replace(
'*', 'x')
for read in samdata.fetch(amplicon_ref, start, end):
rstart = read.reference_start
alignment_length = read.get_overlap(start, end)
#throw out reads that either have gaps in the ROI or don't cover the whole ROI
if alignment_length != expected_length:
continue
if rstart <= start:
qend = qstart = None
for (qpos, rpos) in read.get_aligned_pairs():
if rpos == start:
qstart = qpos
if rpos == end:
qend = qpos
#throw out reads with insertions in the ROI
if not qend or not qstart or qend - qstart != expected_length:
continue
nt_sequence = DNA(read.query_sequence[qstart:qend])
if reverse_comp:
nt_sequence = nt_sequence.reverse_complement()
#scikit-bio doesn't support translating degenerate bases currently, so we will just throw out reads with degenerates for now
if nt_sequence.has_degenerates():
continue
aa_sequence = nt_sequence.translate()
aa_string = str(aa_sequence).replace('*', 'x')
if aa_string:
nt_sequence_counter.update([str(nt_sequence)])
aa_sequence_counter_temp.update([aa_string])
depth += 1
if len(aa_sequence_counter_temp) == 0:
roi_dict['flag'] = "region not found"
return roi_dict
else:
for (aa_string, count) in aa_sequence_counter_temp.most_common():
num_changes = 0
for i in range(len(roi.aa_sequence)):
if len(aa_string) <= i or roi.aa_sequence[i] != aa_string[i]:
num_changes += 1
aa_sequence_counter[(aa_string, num_changes)] = count
#This next bit is just being saved for backward compatibility. Should deprecate and remove soon
(aa_consensus, num_changes) = aa_sequence_counter.most_common(1)[0][0]
nt_consensus = nt_sequence_counter.most_common(1)[0][0]
reference = roi.aa_sequence
consensus = aa_consensus
if roi.nt_sequence:
reference = roi.nt_sequence
consensus = nt_consensus
roi_dict['most_common_aa_sequence'] = aa_consensus
roi_dict['most_common_nt_sequence'] = nt_consensus
roi_dict['reference'] = reference
roi_dict['changes'] = str(num_changes)
#End backward compatibility code
roi_dict['aa_sequence_distribution'] = aa_sequence_counter
roi_dict['nt_sequence_distribution'] = nt_sequence_counter
roi_dict['depth'] = str(depth)
return roi_dict
