Mercurial > repos > tiagoantao > clone_filter
comparison STACKS_clone_filter.py @ 5:1a5ebb16aaea draft
planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty
author | tiagoantao |
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date | Thu, 04 Feb 2016 07:50:26 -0500 |
parents | 42e64fbf4609 |
children | a8b87bc0c3ad |
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4:f4b429a3494a | 5:1a5ebb16aaea |
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1 #!/usr/bin/python | 1 #!/usr/bin/python |
2 # -*- coding: utf-8 -*- | 2 # -*- coding: utf-8 -*- |
3 | 3 |
4 import argparse | |
5 import glob | |
6 import os | |
7 import subprocess | |
4 import shutil | 8 import shutil |
5 import subprocess | |
6 import argparse | |
7 | 9 |
8 | 10 |
9 def __main__(): | 11 def __main__(): |
10 parser = argparse.ArgumentParser() | 12 parser = argparse.ArgumentParser() |
11 parser.add_argument('-f', type=str) | 13 parser.add_argument('-f', type=str) |
18 | 20 |
19 # create the working dir | 21 # create the working dir |
20 os.mkdir('job_outputs') | 22 os.mkdir('job_outputs') |
21 os.chdir('job_outputs') | 23 os.chdir('job_outputs') |
22 | 24 |
23 # STACKS_archive | |
24 # check if zipped files are into the tab | |
25 extract_compress_files(options.P, os.getcwd()) | |
26 | |
27 # create the populations command input line | 25 # create the populations command input line |
28 cmd_line=['clone_filter'] | 26 cmd_line=['clone_filter'] |
29 if options.f is not None: | 27 if options.f is not None: |
30 cmd_line.extend(['-f', options.f]) | 28 cmd_line.extend(['-f', options.f]) |
31 else: | 29 else: |
34 | 32 |
35 print "[CMD]:"+' '.join(cmd_line) | 33 print "[CMD]:"+' '.join(cmd_line) |
36 subprocess.call(cmd_line) | 34 subprocess.call(cmd_line) |
37 | 35 |
38 # postprocesses | 36 # postprocesses |
39 clean_files = glob.glob('*.fq') | 37 clean_files = glob.glob('*.fq*') |
40 if options.f is not None: | 38 if options.f is not None: |
41 shutil.copy(clean_files[0], 'clean.fq') | 39 shutil.copy(clean_files[0], 'clean.fq') |
42 else: | 40 else: |
43 shutil.copy(clean_files[0], 'fwd.fq') | 41 shutil.copy(clean_files[0], 'fwd.fq') |
44 shutil.copy(clean_files[1], 'rev.fq') | 42 shutil.copy(clean_files[1], 'rev.fq') |