[2] | 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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