details: http://www.bx.psu.edu/hg/galaxy/rev/1a56a541f9f9 changeset: 2697:1a56a541f9f9 user: Kelly Vincent <kpvincent@bx.psu.edu> date: Tue Sep 15 14:26:20 2009 -0400 description: In Bowtie wrapper tool, removed --quiet option and redirected stderr to /dev/null 1 file(s) affected in this change: tools/sr_mapping/bowtie_wrapper.py diffs (67 lines): diff -r bd160d40ee15 -r 1a56a541f9f9 tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Tue Sep 15 12:57:17 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.py Tue Sep 15 14:26:20 2009 -0400 @@ -69,10 +69,10 @@ if options.genomeSource == 'history': # set up commands if options.index_settings =='index_pre_set': - indexing_cmds = '--quiet' + indexing_cmds = '' else: try: - indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s --quiet' % \ + indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s' % \ (('','--noauto')[options.iauto_b=='set'], ('','--packed')[options.ipacked=='packed'], ('','--bmax %s'%options.ibmax)[options.ibmax!='None' and options.ibmax>=1], @@ -87,7 +87,7 @@ ('','--cutoff %s'%options.icutoff)[int(options.icutoff)>0], ('','--oldpmap')[options.ioldpmap=='yes']) except ValueError: - indexing_cmds = '--quiet' + indexing_cmds = '' # make temp directory for placement of indices and copy reference file there tmp_dir = tempfile.gettempdir() @@ -96,7 +96,7 @@ except Exception, erf: stop_err('Error creating temp directory for indexing purposes\n' + str(erf)) options.ref = os.path.join(tmp_dir,os.path.split(options.ref)[1]) - cmd1 = 'cd %s; bowtie-build %s -f %s %s' % (tmp_dir, indexing_cmds, options.ref, options.ref) + cmd1 = 'cd %s; bowtie-build %s -f %s %s 2> /dev/null' % (tmp_dir, indexing_cmds, options.ref, options.ref) try: os.system(cmd1) except Exception, erf: @@ -105,11 +105,11 @@ # set up aligning and generate aligning command options # automatically set threads to 8 in both cases if options.params == 'pre_set': - aligning_cmds = '-p %s --quiet' % options.threads + aligning_cmds = '-p %s' % options.threads else: try: aligning_cmds = '%s %s %s %s %s %s %s %s %s %s %s %s %s %s ' \ - '%s %s %s %s %s %s %s %s %s %s %s %s -p %s --quiet' % \ + '%s %s %s %s %s %s %s %s %s %s %s %s -p %s' % \ (('','-s %s'%options.skip)[options.skip!='None'], ('','-u %s'%options.alignLimit)[int(options.alignLimit)>0], ('','-5 %s'%options.trimH)[int(options.trimH)>=0], @@ -138,15 +138,15 @@ ('','--seed %s'%options.seed)[int(options.seed)>=0], options.threads) except ValueError: - aligning_cmds = '-p %s --quiet' % options.threads + aligning_cmds = '-p %s' % options.threads tmp_out = tempfile.NamedTemporaryFile() # prepare actual aligning commands if options.paired == 'paired': - cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % (aligning_cmds, options.ref, options.input1, options.input2, tmp_out.name) + cmd2 = 'bowtie %s %s -1 %s -2 %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.input1, options.input2, tmp_out.name) else: - cmd2 = 'bowtie %s %s %s > %s' % (aligning_cmds, options.ref, options.input1, tmp_out.name) + cmd2 = 'bowtie %s %s %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.input1, tmp_out.name) # prepare command to convert bowtie output to sam and alternative cmd3 = 'bowtie2sam.pl %s > %s' % (tmp_out.name, options.output) cmd4 = 'cp %s %s' % (tmp_out.name, options.output)