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1 #!/usr/bin/env python
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2
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3 """
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4 Move files create by Grinder to a location where it is going to be recognized by
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5 Galaxy as multiple output files with the right format. See
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6 http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple Output Files
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7 Example: python grinder_move_outputs output_dir output_id
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8 Author: Florent Angly
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9 """
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10
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11 import sys, os, re
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12
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13 assert sys.version_info[:2] >= ( 2, 4 )
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14
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15 def stop_err( msg ):
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16 sys.stderr.write( "%s\n" % msg )
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17 sys.exit()
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18
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19 def __main__():
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20 # Get output dir and ID
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21 args = sys.argv
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22 output_dir = args[1]
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23 output_id = args[2]
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24
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25 # Move Grinder files to the proper output
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26 # Grinder filenames look like this
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27 # grinder-ranks.txt
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28 # grinder-reads.fa
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29 # grinder-reads.qual
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30 # grinder-1-ranks.txt
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31 # grinder-1-reads.fa
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32 # grinder-1-reads.qual
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33 # grinder-2-ranks.txt
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34 # grinder-2-reads.fa
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35 # grinder-2-reads.qual
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36
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37 p = re.compile(output_id)
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38 q = re.compile('-(\d+)-')
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39 r = re.compile('-(\w+)$')
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40
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41
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42 for fname in os.listdir(output_dir):
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43
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44 # Skip files that do not start with the output_id
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45 source = os.path.join( output_dir, fname )
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46 basename, extension = os.path.splitext(fname)
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47 if not p.match(fname):
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48 continue
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49
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50 # Assign the dataset format
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51 if extension == '.txt':
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52 format = 'text'
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53 elif extension == '.fa':
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54 format = 'fasta'
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55 elif extension == '.fna':
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56 format = 'fasta'
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57 elif extension == '.faa':
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58 format = 'fasta'
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59 elif extension == '.fasta':
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60 format = 'fasta'
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61 elif extension == '.fq':
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62 format = 'fastq'
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63 elif extension == '.fastq':
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64 format = 'fastq'
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65 elif extension == '.qual':
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66 format = 'qual'
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67 else:
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68 stop_err( 'Error: File %s had the unknown extension %s' % ( fname, extension ) )
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69
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70 # Assign the dataset name
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71 name = ''
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72 match = q.search(basename)
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73 if match != None:
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74 lib_num = match.group(1)
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75 name = 'lib%s' % lib_num
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76
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77 match = r.search(basename)
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78 if match == None:
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79 stop_err( 'Error: File with basename %s did not have a recognized name' % (basename) )
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80
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81 lib_type = match.group(1)
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82 if format == 'qual':
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83 lib_type = 'qual'
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84
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85 name = name + '-' + lib_type
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86
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87 # Move the dataset to the proper place
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88 optional_spec = 'asdf'
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89 destination = os.path.join( output_dir, 'primary_%s_%s_visible_%s_%s' % ( output_id, name, format, optional_spec ) )
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90
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91 print "moving %s to %s" % (source, destination)
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92
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93 try:
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94 os.rename(source, destination)
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95 except Exception, e:
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96 stop_err( 'Error: ' + str( e ) )
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97
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98 if __name__ == "__main__": __main__()
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