text: #! /usr/bin/env python
  import pathogenseq as ps
  import argparse
  
  def main(args):
  	if not args.prefix:
  		ps.log("Please specify prefix with -p")
  		quit(1)
  	if not args.ref:
  		ps.log("Please use --ref to provide a reference... Exiting",ext=T)
  	x= ps.fastq(args.prefix,args.ref,args.r1,args.r2,threads=args.threads)
  	x.illumina(mapper=args.mapper)
  
  parser = argparse.ArgumentParser(description='TBProfiler pipeline',formatter_class=argparse.ArgumentDefaultsHelpFormatter)
  parser.add_argument('--r1','-1', help='First read file')
  parser.add_argument('--r2','-2', help='Second read file')
  parser.add_argument('--ref','-r', help='Reference Sequence')
  parser.add_argument('--threads','-t', type=int, default=1, help='Number of threads')
  parser.add_argument('--prefix','-p', help='Prefix for files')
  parser.add_argument('--mapper','-m', type=str,default="bwa",choices=["bwa","minimap2","bowtie2"],help='Mapping tool to use')
  parser.set_defaults(func=main)
  
  args = parser.parse_args()
  args.func(args)
  