/tools/fastq/fastq_filter.py

https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 34 lines · 26 code · 5 blank · 3 comment · 6 complexity · 9efd2290e126241acc6794f3c060caee MD5 · raw file

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