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1 #
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2 # Pyrocleaner wrapper for galaxy
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3 # Copyright (C) 2009 INRA
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4 #
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5 # This program is free software: you can redistribute it and/or modify
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6 # it under the terms of the GNU General Public License as published by
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7 # the Free Software Foundation, either version 3 of the License, or
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8 # (at your option) any later version.
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9 #
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10 # This program is distributed in the hope that it will be useful,
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 # GNU General Public License for more details.
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14 #
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15 # You should have received a copy of the GNU General Public License
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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17 #
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18 #
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19
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20 __author__ = 'Plateforme bioinformatique Midi Pyrenees'
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21 __copyright__ = 'Copyright (C) 2009 INRA'
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22 __license__ = 'GNU General Public License'
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23 __version__ = '1.2'
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24 __email__ = 'support.genopole@toulouse.inra.fr'
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25 __status__ = 'beta'
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26
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27 import optparse, os, shutil, subprocess, sys, tempfile, re, string
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28
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29 if __name__ == "__main__":
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30
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31 parser = optparse.OptionParser()
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32
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33 parser.add_option( '-s', '--options', dest='options', help='The pyrocleaner options' )
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34 parser.add_option( '-l', '--log', dest='log', help='Path to the pyrocleaner log' )
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35 parser.add_option( '-f', '--format', dest='format', help='The input file format (sff|fastq)' )
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36 parser.add_option( '-o', '--output', dest='output', help='The output file path' )
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37 parser.add_option( '-a', '--out-pe-qual', dest='out_pe_qual', help='The output pairends qual file path' )
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38 parser.add_option( '-b', '--out-pe-fasta', dest='out_pe_fasta', help='The output pairends fasta file path' )
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39 parser.add_option( '-d', '--out-dir', dest='out_dir', help='The output dir where to process the data' )
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40
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41 (options, args) = parser.parse_args()
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42
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43 buffsize = 1048576
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44 tmp_dir = tempfile.mkdtemp()
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45
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46 try:
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47
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48 if options.format == "sff": format = "sff"
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49 else : format = "fastq"
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50
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51 tmp_stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.err' ).name
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52 tmp_stderr = open( tmp_stderr_name, 'wb' )
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53 tmp_stdout_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.out' ).name
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54 tmp_stdout = open( tmp_stdout_name, 'wb' )
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55 cmd = 'pyrocleaner --format %s %s --out %s' % (format, options.options, options.out_dir)
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56 proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno() )
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57 returncode = proc.wait()
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58 tmp_stderr.close()
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59 # get stderr, allowing for case where it's very large
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60 tmp_stderr = open( tmp_stderr_name, 'rb' )
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61 stderr = ''
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62 try:
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63 while True:
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64 stderr += tmp_stderr.read( buffsize )
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65 if not stderr or len( stderr ) % buffsize != 0:
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66 break
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67 except OverflowError:
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68 pass
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69 tmp_stderr.close()
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70 if returncode != 0:
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71 raise Exception, stderr
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72
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73 # Move the log file to the right place
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74 shutil.move(os.path.join(options.out_dir, "pyrocleaner.log"), options.log)
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75
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76 for file in os.listdir(options.out_dir):
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77 # If the file has the input file format and is not a shotgun file
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78 if file.endswith(format):
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79 shutil.move(os.path.join(options.out_dir, file), options.output)
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80 # If it's a quality file from shotgun
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81 if file.endswith(".qual") :
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82 shutil.move(os.path.join(options.out_dir, file), options.out_pe_qual)
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83 # If it's a fasta file from shotgun
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84 elif file.endswith(".fasta") :
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85 shutil.move(os.path.join(options.out_dir, file), options.out_pe_fasta)
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86
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87 except Exception:
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88 raise Exception, 'Error executing pyrocleaner.'
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