def test_golay_module1(self):
"""switching the last base, decode() should recover the original barcode
"""
sent = golay.encode([0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0])
rec = sent[:-1] + 'C' # possible error here
decoded, errors = golay.decode(rec)
self.assertEqual(decoded, sent)
self.assertLessThan(errors, 1.5)
rec = sent[:-1] + 'T' # possible error here
decoded, errors = golay.decode(rec)
self.assertEqual(decoded, sent)
self.assertLessThan(errors, 1.5)
def test_golay_module1(self):
"""switching the last base, decode() should recover the original barcode
"""
sent = golay.encode([0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0])
rec = sent[:-1] + 'C' # possible error here
decoded, errors = golay.decode(rec)
self.assertEqual(decoded, sent)
self.assertLessThan(errors, 1.5)
rec = sent[:-1] + 'T' # possible error here
decoded, errors = golay.decode(rec)
self.assertEqual(decoded, sent)
self.assertLessThan(errors, 1.5)
def main():
args = parser.parse_args()
input_dir = args.input_dir
output_dir = args.output_dir
linker = args.linker
filetype = args.type
i = 0
output_fastx_fp = os.path.join(output_dir,'remultiplexed.' + filetype)
output_fastx = open(output_fastx_fp, 'w')
output_map_fp = os.path.join(output_dir,'remultiplexed_map.' + filetype + '.txt')
output_map = open(output_map_fp, 'w')
output_map.write("#SampleID\tBarcodeSequence\tLinkerPrimerSequence\tReads\tDescription\n")
for fastx in os.listdir(input_dir):
if fastx.endswith(filetype):
try:
fastx_file = open(os.path.join(input_dir,fastx),'Ur')
except IOError:
print "Could not open file ", fastx
continue
i += 1
barcode_seq = encode([int(x) for x in list(str(bin(i))[2:].zfill(12))])
barcode_qual = "I"*12
reads = 0
if filetype in ('fastq','fq','fsq','fnq'):
for header, seq, qual in MinimalFastqParser(fastx_file):
reads += 1
output_fastx.write("@%s\n" % header)
output_fastx.write("{0}{1}\n".format(barcode_seq,seq))
output_fastx.write("+%s\n" % header)
output_fastx.write("{0}{1}\n".format(barcode_qual,qual))
elif filetype in ('fasta','fa','fsa','fna'):
for header, seq in MinimalFastaParser(fastx_file):
reads += 1
output_fastx.write(">%s\n" % header)
output_fastx.write("{0}{1}\n".format(barcode_seq,seq))
output_map.write("{0}\t{1}\t{2}\t{3}\t{4}\n".format(fastx,barcode_seq,linker,reads,fastx))
output_map.close()
output_fastx.close()