Mercurial > repos > tiagoantao > clone_filter
diff STACKS_clone_filter.py @ 5:1a5ebb16aaea draft
planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty
author | tiagoantao |
---|---|
date | Thu, 04 Feb 2016 07:50:26 -0500 |
parents | 42e64fbf4609 |
children | a8b87bc0c3ad |
line wrap: on
line diff
--- a/STACKS_clone_filter.py Wed Feb 03 10:58:13 2016 -0500 +++ b/STACKS_clone_filter.py Thu Feb 04 07:50:26 2016 -0500 @@ -1,9 +1,11 @@ #!/usr/bin/python # -*- coding: utf-8 -*- -import shutil +import argparse +import glob +import os import subprocess -import argparse +import shutil def __main__(): @@ -20,10 +22,6 @@ os.mkdir('job_outputs') os.chdir('job_outputs') - # STACKS_archive - # check if zipped files are into the tab - extract_compress_files(options.P, os.getcwd()) - # create the populations command input line cmd_line=['clone_filter'] if options.f is not None: @@ -36,7 +34,7 @@ subprocess.call(cmd_line) # postprocesses - clean_files = glob.glob('*.fq') + clean_files = glob.glob('*.fq*') if options.f is not None: shutil.copy(clean_files[0], 'clean.fq') else: