/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
- #Dan Blankenberg
- import sys, os, shutil
- from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
- def main():
- #Read command line arguments
- input_filename = sys.argv[1]
- script_filename = sys.argv[2]
- output_filename = sys.argv[3]
- additional_files_path = sys.argv[4]
- input_type = sys.argv[5] or 'sanger'
-
- #Save script file for debuging/verification info later
- os.mkdir( additional_files_path )
- shutil.copy( script_filename, os.path.join( additional_files_path, 'debug.txt' ) )
-
- out = fastqWriter( open( output_filename, 'wb' ), format = input_type )
-
- i = None
- reads_kept = 0
- for i, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
- local = {'fastq_read':fastq_read, 'ret_val':False}
- execfile( script_filename, {}, local )
- if local['ret_val']:
- out.write( fastq_read )
- reads_kept += 1
- out.close()
- if i is None:
- print "Your file contains no valid fastq reads."
- else:
- print 'Kept %s of %s reads (%.2f%%).' % ( reads_kept, i + 1, float( reads_kept ) / float( i + 1 ) * 100.0 )
- if __name__ == "__main__":
- main()