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1 #Dan Blankenberg
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2 import sys, os, shutil
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3 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
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4
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5 def main():
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6 #Read command line arguments
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7 input_filename = sys.argv[1]
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8 script_filename = sys.argv[2]
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9 output_filename = sys.argv[3]
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10 additional_files_path = sys.argv[4]
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11 input_type = sys.argv[5] or 'sanger'
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12
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13 #Save script file for debuging/verification info later
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14 os.mkdir( additional_files_path )
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15 shutil.copy( script_filename, os.path.join( additional_files_path, 'debug.txt' ) )
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16
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17 out = fastqWriter( open( output_filename, 'wb' ), format = input_type )
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18
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19 i = None
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20 reads_kept = 0
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21 for i, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
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22 local = {'fastq_read':fastq_read, 'ret_val':False}
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23 execfile( script_filename, {}, local )
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24 if local['ret_val']:
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25 out.write( fastq_read )
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26 reads_kept += 1
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27 out.close()
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28 if i is None:
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29 print "Your file contains no valid fastq reads."
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30 else:
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31 print 'Kept %s of %s reads (%.2f%%).' % ( reads_kept, i + 1, float( reads_kept ) / float( i + 1 ) * 100.0 )
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32
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33 if __name__ == "__main__":
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34 main()
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