root/galaxy-central/tools/fastq/fastq_manipulation.py

#Dan Blankenberg
import sys, os, shutil
import imp
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' ) )
    
    fastq_manipulator = imp.load_module( 'fastq_manipulator', open( script_filename ), script_filename, ( '', 'r', imp.PY_SOURCE ) )
    
    out = fastqWriter( open( output_filename, 'wb' ), format = input_type )
    
    i = None
    reads_manipulated = 0
    for i, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
        new_read = fastq_manipulator.match_and_manipulate_read( fastq_read )
        if new_read:
            out.write( new_read )
        if new_read != fastq_read:
            reads_manipulated += 1
    out.close()
    if i is None:
        print "Your file contains no valid FASTQ reads."
    else:
        print 'Manipulated %s of %s reads (%.2f%%).' % ( reads_manipulated, i + 1, float( reads_manipulated ) / float( i + 1 ) * 100.0 )

if __name__ == "__main__":
    main()