Mercurial > repos > xuebing > sharplabtool
view tools/next_gen_conversion/solid_to_fastq.py @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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#!/usr/bin/env python """ Converts SOLiD data to Sanger FASTQ format. usage: %prog [options] -i, --input1=i: Forward reads file -q, --input2=q: Forward qual file -I, --input3=I: Reverse reads file -Q, --input4=Q: Reverse qual file -o, --output1=o: Forward output -r, --output2=r: Reverse output usage: %prog forward_reads_file forwards_qual_file reverse_reads_file(or_None) reverse_qual_file(or_None) output_file ouptut_id output_dir """ import os, sys, tempfile from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) from bx.cookbook import doc_optparse def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) sys.exit() def replaceNeg1(fin, fout): line = fin.readline() while line.strip(): fout.write(line.replace('-1', '1')) line = fin.readline() fout.seek(0) return fout def __main__(): #Parse Command Line options, args = doc_optparse.parse( __doc__ ) # common temp file setup tmpf = tempfile.NamedTemporaryFile() #forward reads tmpqf = tempfile.NamedTemporaryFile() tmpqf = replaceNeg1(file(options.input2,'r'), tmpqf) # if paired-end data (have reverse input files) if options.input3 != "None" and options.input4 != "None": tmpr = tempfile.NamedTemporaryFile() #reverse reads # replace the -1 in the qualities file tmpqr = tempfile.NamedTemporaryFile() tmpqr = replaceNeg1(file(options.input4,'r'), tmpqr) cmd1 = "%s/bwa_solid2fastq_modified.pl 'yes' %s %s %s %s %s %s 2>&1" %(os.path.split(sys.argv[0])[0], tmpf.name, tmpr.name, options.input1, tmpqf.name, options.input3, tmpqr.name) try: os.system(cmd1) os.system('gunzip -c %s >> %s' %(tmpf.name,options.output1)) os.system('gunzip -c %s >> %s' %(tmpr.name,options.output2)) except Exception, eq: stop_err("Error converting data to fastq format.\n" + str(eq)) tmpr.close() tmpqr.close() # if single-end data else: cmd1 = "%s/bwa_solid2fastq_modified.pl 'no' %s %s %s %s %s %s 2>&1" % (os.path.split(sys.argv[0])[0], tmpf.name, None, options.input1, tmpqf.name, None, None) try: os.system(cmd1) os.system('gunzip -c %s >> %s' % (tmpf.name, options.output1)) except Exception, eq: stop_err("Error converting data to fastq format.\n" + str(eq)) tmpqf.close() tmpf.close() sys.stdout.write('converted SOLiD data') if __name__=="__main__": __main__()