--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/fastq_groomer_parallel.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,115 @@
+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()