/tools/fastq/fastq_trimmer.py

https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 41 lines · 37 code · 3 blank · 1 comment · 13 complexity · a13c4e0f582e56c1766d1aaf0d8a7990 MD5 · raw file

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