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1 #Dan Blankenberg
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2 import sys
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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 input_filename = sys.argv[1]
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7 output_filename = sys.argv[2]
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8 left_offset = sys.argv[3]
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9 right_offset = sys.argv[4]
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10 percent_offsets = sys.argv[5] == 'offsets_percent'
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11 input_type = sys.argv[6] or 'sanger'
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12 keep_zero_length = sys.argv[7] == 'keep_zero_length'
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13
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14 out = fastqWriter( open( output_filename, 'wb' ), format = input_type )
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15 num_reads_excluded = 0
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16 num_reads = None
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17 for num_reads, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
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18 if percent_offsets:
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19 left_column_offset = int( round( float( left_offset ) / 100.0 * float( len( fastq_read ) ) ) )
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20 right_column_offset = int( round( float( right_offset ) / 100.0 * float( len( fastq_read ) ) ) )
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21 else:
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22 left_column_offset = int( left_offset )
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23 right_column_offset = int( right_offset )
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24 if right_column_offset > 0:
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25 right_column_offset = -right_column_offset
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26 else:
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27 right_column_offset = None
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28 fastq_read = fastq_read.slice( left_column_offset, right_column_offset )
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29 if keep_zero_length or len( fastq_read ):
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30 out.write( fastq_read )
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31 else:
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32 num_reads_excluded += 1
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33 out.close()
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34 if num_reads is None:
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35 print "No valid fastq reads could be processed."
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36 else:
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37 print "%i fastq reads were processed." % ( num_reads + 1 )
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38 if num_reads_excluded:
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39 print "%i reads of zero length were excluded from the output." % num_reads_excluded
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40
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41 if __name__ == "__main__": main()
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