help='Name of the adapter set',
required=True,
choices=sorted(tagdigger_fun.adapters.keys()))
args = parser.parse_args()
bckeys = tagdigger_fun.readBarcodeKeyfile(args.barcodefile, forSplitter=True)
if bckeys == None:
raise Exception("Problem reading barcode file.")
adapter = tagdigger_fun.adapters[args.adapter]
enzyme = args.adapter[:args.adapter.find("-")]
cutsite = tagdigger_fun.enzymes[enzyme]
fqfiles = sorted(bckeys.keys())
fqok = [tagdigger_fun.isFastq(f) for f in fqfiles]
if not all(fqok):
print("Cannot read the following as FASTQ files:")
print([fqfiles[i] for i in range(len(fqfiles)) if not fqok[i]])
raise Exception("Cannot read all FASTQ files.")
for f in fqfiles:
tagdigger_fun.barcodeSplitter(f,
bckeys[f][0],
bckeys[f][1],
cutsite=cutsite,
adapter=adapter)
thisdircontents = os.listdir('.')
for i in thisdircontents:
print(i)
# read in key file
bckeys = None
while bckeys == None:
bckeys = tagdigger_fun.readBarcodeKeyfile(input("\nName of key file with barcodes: ").strip(), forSplitter=True)
# summarize
fqfiles = sorted(bckeys.keys())
for f in fqfiles:
print("File {}: {} barcodes".format(f, len(bckeys[f][0])))
print("")
# check that FASTQ files are okay
fqok = [tagdigger_fun.isFastq(f) for f in fqfiles]
while not all(fqok):
print("Cannot read the following as FASTQ files:")
for f in range(len(fqok)):
if not fqok[f]:
print(fqfiles[f])
thischoice = '0'
while thischoice not in {'1', '2', '3'}:
thischoice = input('''
Press 1 to re-read key file, 2 to search for FASTQ files in a different
directory, or 3 to try reading the same FASTQ files again: ''').strip()
if thischoice == '1':
bckeys = None
while bckeys == None:
bckeys = tagdigger_fun.readBarcodeKeyfile(input("\nName of key file with barcodes: "))
fqfiles = sorted(bckeys.keys())