barcode_splitter_script.py

#!/usr/bin/env python3

# non-interactive script for doing barcode splitting

import tagdigger_fun
import argparse

parser = argparse.ArgumentParser(description="TagDigger v. 1.1 barcode splitter command line script by Lindsay V. Clark")
parser.add_argument('-b', '--barcodefile', help = 'Name of barcode key file',
                    required = True)
parser.add_argument('-a', '--adapter', 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)