Mercurial > repos > tiagoantao > clone_filter
view STACKS_clone_filter.py @ 12:7a8369cfa7c1 draft default tip
planemo upload commit 9b504bd948d6079168cbd5cf6f9aa5e5488cde9b-dirty
author | tiagoantao |
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date | Wed, 10 Feb 2016 14:04:19 -0500 |
parents | 92ba49d68ef1 |
children |
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#!/usr/bin/python # -*- coding: utf-8 -*- import argparse import glob import os import subprocess import shutil def __main__(): parser = argparse.ArgumentParser() #files (single or pair) parser.add_argument('-f', type=str) parser.add_argument('-fwd', type=str) parser.add_argument('-rev', type=str) #oligos parser.add_argument('-oligo_len_1', type=int) parser.add_argument('-oligo_len_2', type=int) #options (allways there) parser.add_argument('-opt', type=str) #parser.add_argument('-k', action='store_true') options = parser.parse_args() # create the working dir os.mkdir('job_outputs') os.chdir('job_outputs') # create the populations command input line cmd_line=['clone_filter'] if options.f is not None: cmd_line.extend(['-f', options.f]) else: cmd_line.extend(['-1', options.fwd]) cmd_line.extend(['-2', options.rev]) if options.oligo_len_1 > -1: cmd_line.extend(['--oligo_len_1', options.oligo_len_1]) if options.oligo_len_2 > -1: cmd_line.extend(['--oligo_len_2', options.oligo_len_2]) cmd_line.append('--' + options.opt) print "[CMD]:"+' '.join(cmd_line) subprocess.call(cmd_line) # postprocesses clean_files = glob.glob('*.fq*') if options.f is not None: shutil.copy(clean_files[0], 'clean.fq') else: shutil.copy(clean_files[0], 'fwd.fq') shutil.copy(clean_files[1], 'rev.fq') if __name__ == '__main__': __main__()