def demultiplex(f, barcodes, extract_barcode):
d = Demultiplexer(BarcodeWriterFactory(sys.argv[2]), barcodes,
extract_barcode)
f = SeqIO.parse_fastq(SeqIO.Open(input_file, "r"))
cnt = 0
for record in f:
cnt += 1
d.write(record)
d.close()
f.close()
def CollectBarcodes(f, extract_barcode):
h = SeqIO.parse_fastq(SeqIO.Open(f, "r"))
cnt = 0
counter = dict()
for record in h:
barcode = extract_barcode(record)
if barcode not in counter:
counter[barcode] = 0
counter[barcode] += 1
cnt += 1
if cnt == 100000:
break
return [barcode for barcode, count in counter.iteritems() if count >= 100]
