def action(args):
barcodes = get_barcodes(args.barcodes)
bc_seqs, bc_labels = zip(*barcodes)
bc_dict = dict(barcodes)
bc_rexp = re.compile('|'.join(bc_seqs))
opener = bz2.BZ2File if args.fastq.endswith('.bz2') else open
count = Counter()
with opener(args.fastq) as f, bz2.BZ2File(args.mapfile, 'w') as mapout:
writer = csv.writer(mapout)
writer.writerow([
'name', 'label', 'barcode', 'ratio', 'bc_start', 'bc_stop', 'rle'
])
for seq in SeqIO.parse(f, 'fastq'):
if not args.min_length <= len(seq) <= args.max_length:
count['fail_len'] += 1
continue
barcode, ratio, bc_start, bc_stop = find_barcode(
seq,
bc_rexp,
bc_seqs,
exact=False,
bc_len=10,
search_window=args.search_window)
sample = bc_dict.get(barcode)
name = seq.id.replace(':', '_')
if barcode:
if count['matched'] >= args.limit:
break
count['matched'] += 1
count[barcode] += 1
seq, counts = homoencode(seq.seq)
args.outfile.write('>%s %s\n%s\n' % (name, sample, seq))
writer.writerow([
name, sample, barcode, ratio, bc_start, bc_stop,
to_ascii(counts)
])
elif args.unmatched:
count['no_match'] += 1
args.unmatched.write('>%s\n%s\n' % (name, seq.seq))
writer.writerow(
[name, sample, None, barcode, ratio, bc_start, bc_stop])
stats = csv.writer(args.stats)
rows = sorted((bc_dict[k], v) for k, v in count.items() if k in bc_dict)
stats.writerows(rows)
stats.writerow(['total_matched', count['matched']])
stats.writerow(['no_match', count['no_match']])
stats.writerow(['fail_len', count['fail_len']])
def action(args):
barcodes = get_barcodes(args.barcodes)
bc_seqs, bc_labels = zip(*barcodes)
bc_dict = dict(barcodes)
bc_rexp = re.compile('|'.join(bc_seqs))
opener = bz2.BZ2File if args.fastq.endswith('.bz2') else open
count = Counter()
with opener(args.fastq) as f, bz2.BZ2File(args.mapfile, 'w') as mapout:
writer = csv.writer(mapout)
writer.writerow(['name','label','barcode','ratio','bc_start','bc_stop','rle'])
for seq in SeqIO.parse(f, 'fastq'):
if not args.min_length <= len(seq) <= args.max_length:
count['fail_len'] += 1
continue
barcode, ratio, bc_start, bc_stop = find_barcode(
seq, bc_rexp, bc_seqs,
exact = False,
bc_len = 10,
search_window = args.search_window)
sample = bc_dict.get(barcode)
name = seq.id.replace(':','_')
if barcode:
if count['matched'] >= args.limit:
break
count['matched'] += 1
count[barcode] += 1
seq, counts = homoencode(seq.seq)
args.outfile.write('>%s %s\n%s\n' % (name, sample, seq))
writer.writerow([name, sample, barcode, ratio, bc_start, bc_stop, to_ascii(counts)])
elif args.unmatched:
count['no_match'] += 1
args.unmatched.write('>%s\n%s\n' % (name, seq.seq))
writer.writerow([name, sample, None, barcode, ratio, bc_start, bc_stop])
stats = csv.writer(args.stats)
rows = sorted((bc_dict[k], v) for k, v in count.items() if k in bc_dict)
stats.writerows(rows)
stats.writerow(['total_matched', count['matched']])
stats.writerow(['no_match', count['no_match']])
stats.writerow(['fail_len', count['fail_len']])
def seq_and_homoencode(seq):
return seq, homoencode(seq.seq)
def seq_and_homoencode(seq):
return seq, homoencode(seq.seq)
def test02(self):
rle, counts = sequtils.homoencode('GCTTCAAACATA')
self.assertEquals(rle, 'GCTCACATA')
self.assertEquals(counts, [1, 1, 2, 1, 3, 1, 1, 1, 1])
def test01(self):
rle, counts = sequtils.homoencode('AAA')
self.assertEquals(rle, 'A')
self.assertEquals(counts, [3])
def test01(self):
seq = 'TCTGGACCGTGTCTTTCAGTTCCAAAGTGTGACTGATCCATCCTCTCAGACC'
e, c = sequtils.homoencode(seq)
self.assertEquals(seq, sequtils.homodecode(e, c))