def go(args):
bed = read_bed_file(args.bedfile)
infile = pysam.AlignmentFile(args.alignment, "rb")
for s in infile:
#print s.get_aligned_pairs()
#print ">%s\n%s" % (s.query_name, s.query_alignment_sequence)
p1 = find_primer(bed, s.reference_start, '+')
p2 = find_primer(bed, s.reference_end, '-')
primer_start = p1[2]['start']
# start is the 5'
primer_end = p2[2]['start']
query_align_start = find_query_pos(s, primer_start)
query_align_end = find_query_pos(s, primer_end)
print >> sys.stderr, "%s\t%s\t%s\t%s" % (primer_start, primer_end,
primer_end - primer_start,
s.query_length)
startpos = max(0, query_align_start - 40)
endpos = min(query_align_end + 40, s.query_length)
print ">%s\n%s" % (s.query_name, s.query_sequence[startpos:endpos])
def go(args):
if args.report:
reportfh = open(args.report, "w")
bed = read_bed_file(args.bedfile)
counter = defaultdict(int)
infile = pysam.AlignmentFile("-", "rb")
outfile = pysam.AlignmentFile("-", "wh", template=infile)
for s in infile:
cigar = copy(s.cigartuples)
## logic - if alignment start site is _before_ but within X bases of
## a primer site, trim it off
if s.is_unmapped:
sys.stderr.write("%s skipped as unmapped" % (s.query_name))
continue
if s.is_supplementary:
sys.stderr.write("%s skipped as supplementary" % (s.query_name))
continue
p1 = find_primer(bed, s.reference_start, '+')
p2 = find_primer(bed, s.reference_end, '-')
report = "%s\t%s\t%s\t%s_%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" % (
s.query_name, s.reference_start, s.reference_end,
p1[2]['Primer_ID'], p2[2]['Primer_ID'], p1[2]['Primer_ID'],
abs(p1[1]), p2[2]['Primer_ID'], abs(p2[1]), s.is_secondary,
s.is_supplementary, p1[2]['start'], p2[2]['end'])
if args.report:
print(report, file=reportfh)
if args.verbose:
sys.stderr.write(report)
## if the alignment starts before the end of the primer, trim to that position
try:
if args.start:
primer_position = p1[2]['start']
else:
primer_position = p1[2]['end']
if s.reference_start < primer_position:
trim(cigar, s, primer_position, 0)
else:
if args.verbose:
sys.stderr.write("ref start %s >= primer_position %s" %
(s.reference_start, primer_position))
if args.start:
primer_position = p2[2]['start']
else:
primer_position = p2[2]['end']
if s.reference_end > primer_position:
trim(cigar, s, primer_position, 1)
else:
if args.verbose:
sys.stderr.write("ref end %s >= primer_position %s" %
(s.reference_end, primer_position))
except Exception as e:
sys.stderr.write("problem %s" % (e, ))
pass
if args.normalise:
pair = "%s-%s-%d" % (p1[2]['Primer_ID'], p2[2]['Primer_ID'],
s.is_reverse)
counter[pair] += 1
if counter[pair] > args.normalise:
continue
## if the alignment starts before the end of the primer, trim to that position
# trim(s, s.reference_start + 40, 0)
# trim(s, s.reference_end - 40, 1)
#
# outfile.write(s)
# except Exception:
# pass
if not check_still_matching_bases(s):
continue
outfile.write(s)
reportfh.close()
if not end:
s.pos = pos - extra
#print >>sys.stderr, "New pos: %s" % (s.pos)
if end:
cigar.append((4, eaten))
else:
cigar.insert(0, (4, eaten))
oldcigarstring = s.cigarstring
s.cigartuples = cigar
#print >>sys.stderr, s.query_name, oldcigarstring[0:50], s.cigarstring[0:50]
bed = read_bed_file('all')
def find_primer(pos, direction):
# {'Amplicon_size': '1874', 'end': 7651, '#Region': 'region_4', 'start': 7633, 'Coords': '7633', "Sequence_(5-3')": 'GCTGGCCCGAAATATGGT', 'Primer_ID': '16_R'}
from operator import itemgetter
closest = min([(abs(p['start'] - pos), p['start'] - pos, p)
for p in bed if p['direction'] == direction],
key=itemgetter(0))
return closest
infile = pysam.AlignmentFile("-", "rb")
outfile = pysam.AlignmentFile("-", "wh", template=infile)
for s in infile:
if not end:
s.pos = pos - extra
#print >>sys.stderr, "New pos: %s" % (s.pos)
if end:
cigar.append((4, eaten))
else:
cigar.insert(0, (4, eaten))
oldcigarstring = s.cigarstring
s.cigartuples = cigar
#print >>sys.stderr, s.query_name, oldcigarstring[0:50], s.cigarstring[0:50]
bed = read_bed_file('all')
def find_primer(pos, direction):
# {'Amplicon_size': '1874', 'end': 7651, '#Region': 'region_4', 'start': 7633, 'Coords': '7633', "Sequence_(5-3')": 'GCTGGCCCGAAATATGGT', 'Primer_ID': '16_R'}
from operator import itemgetter
closest = min([(abs(p['start'] - pos), p['start'] - pos, p) for p in bed if p['direction'] == direction], key=itemgetter(0))
return closest
infile = pysam.AlignmentFile("-", "rb")
outfile = pysam.AlignmentFile("-", "wh", template=infile)
for s in infile:
cigar = copy(s.cigartuples)
if len(sys.argv) > 1:
if not s.query_name.startswith(sys.argv[1]):
#MASKED_POSITIONS.extend([n for n in xrange(17135, 17169)])
#MASKED_POSITIONS.extend([n for n in xrange(5742, 5758)])
#MASKED_POSITIONS = [2282, 14011, 5312, 5313]
#MASKED_POSITIONS = [2282, 11973]
MASKED_POSITIONS = [2282]
reference = sys.argv[1]
vcffile = sys.argv[2]
bamfile = sys.argv[3]
primerset = sys.argv[4]
#MASKED_POSITIONS.extend([int(n) for n in sys.argv[5].split(",")])
DEPTH_THRESHOLD = 25
bed = read_bed_file(primerset)
for primer in bed:
MASKED_POSITIONS.extend([n for n in xrange(primer['start'], primer['end'])])
def collect_depths(bamfile):
if not os.path.exists(bamfile):
raise SystemExit("bamfile %s doesn't exist" % (bamfile,))
print >>sys.stderr, bamfile
p = subprocess.Popen(['samtools', 'depth', bamfile],
stdout=subprocess.PIPE)
out, err = p.communicate()
depths = defaultdict(dict)
for ln in out.split("\n"):
if ln:
