Mercurial > repos > bgruening > bismark
annotate bismark_deduplicate/bismark_deduplicate_wrapper.py @ 7:fcadce4d9a06 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author | bgruening |
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date | Sat, 06 May 2017 13:18:09 -0400 |
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7
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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1 #!/usr/bin/python |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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2 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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3 import argparse |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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4 import os |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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5 import re |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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6 import shutil |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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7 import subprocess |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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8 import sys |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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9 import tempfile |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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10 import logging |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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11 from glob import glob |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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12 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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13 def cleanup_before_exit(tmp_dir): |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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14 if tmp_dir and os.path.exists(tmp_dir): |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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15 shutil.rmtree(tmp_dir) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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16 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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17 def get_arg(): |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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18 parser = argparse.ArgumentParser() |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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19 parser.add_argument('--tool_dir', dest='tool_dir', action='store', nargs=1, metavar='tool_dir', type=str) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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20 parser.add_argument('-p', action='store_true') |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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21 parser.add_argument('-s', action='store_true') |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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22 parser.add_argument('--input', dest='input', action='store', nargs=1, metavar='input', type=str) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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23 parser.add_argument('--output_report', dest='output_report', action='store', nargs=1, metavar='output_report', type=str) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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24 parser.add_argument('--output_bam', dest='output_bam', action='store', nargs=1, metavar='output_report', type=str) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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25 parser.add_argument('--log_report', dest='log_report', action='store', nargs=1, metavar='log_filename', type=str) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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26 args = parser.parse_args() |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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27 return args |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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28 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
diff
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29 def __main__(): |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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30 args = get_arg() |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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31 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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32 tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='') |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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33 os.chdir(tmp_dir) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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34 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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35 if args.log_report: |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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36 logging.basicConfig(level=logging.INFO, filename=args.log_report[0], filemode="a+", format='%(message)s') |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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37 else: |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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38 logging.basicConfig(level=logging.INFO, filename=os.path.join(tmp_dir, 'log_report.txt'), filemode="a+", format='%(message)s') |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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39 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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40 default_reads_name = 'submitted_reads.bam' |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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41 os.symlink(args.input[0], default_reads_name) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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42 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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43 if args.p is True: |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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44 sPaired = '-p' |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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45 if args.s is True: |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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46 sPaired = '-s' |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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47 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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48 cmd = 'perl %s %s duplicated_reads.bam --bam' % (os.path.join(args.tool_dir[0], 'deduplicate_bismark'), sPaired) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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49 logging.info('COMMAND LINE:\n\n%s' % cmd) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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50 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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51 proc = subprocess.Popen(['perl', os.path.join(args.tool_dir[0], 'deduplicate_bismark'), sPaired, default_reads_name, '--bam'], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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52 proc_out, proc_err = proc.communicate() |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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53 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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54 logging.info("__________________________________________________________________\n") |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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55 logging.info("BISMARK DEDUPLICATE STDOUT:\n\n%s" % proc_out) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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56 if proc_err: |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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57 logging.critical("__________________________________________________________________\n") |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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58 logging.critical("BISMARK DEDUPLICATE WARNING:\n\n%s" % proc_err) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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59 sys.exit("Dedpulicate Bismark crashed with the folowing error message:\n%s" % proc_err) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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60 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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61 shutil.move( glob('*deduplicated.bam')[0], args.output_bam[0] ) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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62 shutil.move( glob('*deduplication_report.txt')[0], args.output_report[0]) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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63 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents:
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64 cleanup_before_exit(tmp_dir) |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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65 |
fcadce4d9a06
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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66 if __name__=="__main__": __main__() |