Mercurial > repos > tiagoantao > clone_filter
annotate STACKS_clone_filter.py @ 3:7f57bdd5138d draft
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author | tiagoantao |
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date | Wed, 03 Feb 2016 10:51:05 -0500 |
parents | 42e64fbf4609 |
children | 1a5ebb16aaea |
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1 #!/usr/bin/python |
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2 # -*- coding: utf-8 -*- |
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3 |
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4 import shutil |
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5 import subprocess |
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6 import argparse |
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7 |
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8 |
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9 def __main__(): |
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10 parser = argparse.ArgumentParser() |
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11 parser.add_argument('-f', type=str) |
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12 parser.add_argument('-fwd', type=str) |
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13 parser.add_argument('-rev', type=str) |
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14 |
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15 #parser.add_argument('-k', action='store_true') |
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16 |
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17 options = parser.parse_args() |
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18 |
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19 # create the working dir |
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20 os.mkdir('job_outputs') |
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21 os.chdir('job_outputs') |
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22 |
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23 # STACKS_archive |
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24 # check if zipped files are into the tab |
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25 extract_compress_files(options.P, os.getcwd()) |
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26 |
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27 # create the populations command input line |
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28 cmd_line=['clone_filter'] |
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29 if options.f is not None: |
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30 cmd_line.extend(['-f', options.f]) |
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31 else: |
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32 cmd_line.extend(['-1', options.fwd]) |
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33 cmd_line.extend(['-2', options.rev]) |
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34 |
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35 print "[CMD]:"+' '.join(cmd_line) |
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36 subprocess.call(cmd_line) |
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37 |
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38 # postprocesses |
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39 clean_files = glob.glob('*.fq') |
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40 if options.f is not None: |
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41 shutil.copy(clean_files[0], 'clean.fq') |
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42 else: |
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43 shutil.copy(clean_files[0], 'fwd.fq') |
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44 shutil.copy(clean_files[1], 'rev.fq') |
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45 |
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46 |
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47 if __name__ == '__main__': |
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48 __main__() |