view SMART/DiffExpAnal/fastq_groomer_parallel.py @ 31:0ab839023fe4

Uploaded

import sys, os, optparse, random
from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter

def stop_err(msg):
	sys.stderr.write("%s\n" % msg)
	sys.exit()

def main():

    input_filename = sys.argv[1]  #a txt file
    input_type = sys.argv[2]
    output_filename = sys.argv[3] #a txt file
    output_type = sys.argv[4]
    force_quality_encoding = sys.argv[5]
    summarize_input = sys.argv[6] == 'summarize_input'
    pairedEnd_input = sys.argv[7] 
    if pairedEnd_input == 'None':
	    pairedEnd_input = None
    else:
	output_pairedEndFileName = sys.argv[8]

    if force_quality_encoding == 'None':
        force_quality_encoding = None

    #Parse the input txt file and read a list of fastq files
    file = open(input_filename, "r")
    lines = file.readlines()
    inputFileNames = []
    outGroomerNames = []
    resDirName = os.path.dirname(output_filename) + "/"
    #Write output txt file and define all output groomer file names
    outFile = open(output_filename, "w")
    for line in lines:
		tab = line.split()
		inputFileNames.append(tab[1])
		outGroomerName = resDirName + tab[0] + '_outGroomer_%s.fastq' % random.randrange(0, 10000)
		outGroomerNames.append(outGroomerName)
		outFile.write(tab[0] + '\t' + outGroomerName + '\n')
    outFile.close()
    file.close()

    if pairedEnd_input != None:
	inPairedFile = open(pairedEnd_input, "r")
	lines = inPairedFile.readlines()
	inputPairedEndFileNames = []
	outGroomerPairedEndNames = []
	outPairedEndFile = open(output_pairedEndFileName, "w")
	for line in lines:
		tab = line.split()
		inputPairedEndFileNames.append(tab[1])
		outGroomerPairedEndName = resDirName + tab[0] + '_outGroomer_pairedEnd_%s.fastq' % random.randrange(0, 10000)
		outGroomerPairedEndNames.append(outGroomerPairedEndName)
		outPairedEndFile.write(tab[0] + '\t' + outGroomerPairedEndName + '\n')
	outPairedEndFile.close()
        inPairedFile.close()
    
    # Write output file
    aggregator = fastqAggregator()
    for i in range(len(outGroomerNames)):
	out = fastqWriter( open( outGroomerNames[i], 'wb' ), format = output_type, force_quality_encoding = force_quality_encoding )
	read_count = None
	if summarize_input:
	    reader = fastqVerboseErrorReader
	else:
	    reader = fastqReader
	for read_count, fastq_read in enumerate( reader( open( inputFileNames[i] ), format = input_type, apply_galaxy_conventions = True ) ):
	    if summarize_input:
	        aggregator.consume_read( fastq_read )
	    out.write( fastq_read )
	out.close()
	    
	if read_count is not None:
	    print "Groomed %i %s reads into %s reads." % ( read_count + 1, input_type, output_type )
	    if input_type != output_type and 'solexa' in [ input_type, output_type ]:
	        print "Converted between Solexa and PHRED scores."
	    if summarize_input:
	        print "Based upon quality and sequence, the input data is valid for: %s" % ( ", ".join( aggregator.get_valid_formats() )  or "None" )
	        ascii_range = aggregator.get_ascii_range()
	        decimal_range =  aggregator.get_decimal_range()
	        print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( ascii_range[0] ), ord( ascii_range[0] ), repr( ascii_range[1] ), ord( ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed
	        print "Input decimal range: %i - %i" % ( decimal_range[0], decimal_range[1] )        
	else:
	     print "No valid FASTQ reads were provided."


    # Write output pairedEnd file
    if pairedEnd_input != None:
	    aggregator = fastqAggregator()
	    for i in range(len(outGroomerPairedEndNames)):
		    outPair = fastqWriter(open(outGroomerPairedEndNames[i], 'wb'), format = output_type, force_quality_encoding = force_quality_encoding)
		    read_count = None
		    if summarize_input:
			    reader = fastqVerboseErrorReader
		    else:
			    reader = fastqReader
		    for read_count, fastq_reader in enumerate(reader(open(inputPairedEndFileNames[i]), format=input_type, apply_galaxy_conventions=True)):
				   if summarize_input:
				   	aggregator.consume_read(fastq_read)
				   outPair.write(fastq_read)
		    outPair.close()

		    if read_count is not None:
		    	print "Groomed %i %s reads into %s reads." % ( read_count + 1, input_type, output_type )
		    if input_type != output_type and 'solexa' in [ input_type, output_type ]:
		   	print "Converted between Solexa and PHRED scores."
		    if summarize_input:
		   	print "Based upon quality and sequence, the input data is valid for: %s" % ( ", ".join( aggregator.get_valid_formats() )  or "None" )
			ascii_range = aggregator.get_ascii_range()
			decimal_range =  aggregator.get_decimal_range()
			print "Input ASCII range: %s(%i) - %s(%i)" % ( repr( ascii_range[0] ), ord( ascii_range[0] ), repr( ascii_range[1] ), ord( ascii_range[1] ) ) #print using repr, since \x00 (null) causes info truncation in galaxy when printed
			print "Input decimal range: %i - %i" % ( decimal_range[0], decimal_range[1] )
		    else:
		   	 print "No valid paired-end FASTQ reads were provided."

if __name__ == "__main__": main()