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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 ## Dan, Others: Can we simply drop the "format=input_type" here since it is specified in reader.
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18 ## This optimization would cut runtime roughly in half (for my test case anyway). -John
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19 out = fastqWriter( open( output_filename, 'wb' ), format = input_type )
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20
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21 i = None
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22 reads_kept = 0
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23 execfile(script_filename, globals())
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24 for i, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
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25 ret_val = fastq_read_pass_filter( fastq_read ) ## fastq_read_pass_filter defined in script_filename
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26 if ret_val:
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27 out.write( fastq_read )
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28 reads_kept += 1
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29 out.close()
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30 if i is None:
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31 print "Your file contains no valid fastq reads."
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32 else:
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33 print 'Kept %s of %s reads (%.2f%%).' % ( reads_kept, i + 1, float( reads_kept ) / float( i + 1 ) * 100.0 )
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34
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35 if __name__ == "__main__":
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36 main()
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