details: http://www.bx.psu.edu/hg/galaxy/rev/e58e140b89f7 changeset: 2689:e58e140b89f7 user: Kelly Vincent <kpvincent@bx.psu.edu> date: Mon Sep 14 14:54:11 2009 -0400 description: Updated Bowtie wrapper tool to add a number of threads parameter and remove two unnecessary options 2 file(s) affected in this change: tools/sr_mapping/bowtie_wrapper.py tools/sr_mapping/bowtie_wrapper.xml diffs (198 lines): diff -r 7f4c8fee3b39 -r e58e140b89f7 tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Mon Sep 14 12:23:16 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.py Mon Sep 14 14:54:11 2009 -0400 @@ -13,6 +13,7 @@ def __main__(): #Parse Command Line parser = optparse.OptionParser() + parser.add_option('', '--threads', dest='threads', help='The number of threads to run') parser.add_option('', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format') parser.add_option('', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format') parser.add_option('', '--output', dest='output', help='The output file') @@ -35,7 +36,6 @@ parser.add_option('', '--offbase', dest='offbase', help='Number the first base of a reference sequence as n when outputting alignments') parser.add_option('', '--best', dest='best', help="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions") parser.add_option('', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read') - parser.add_option('', '--threadMem', dest='threadMem', help='Number of megabytes of memory a given thread is given to store path descriptors in best mode') parser.add_option('', '--strata', dest='strata', help='Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable') parser.add_option('', '--minInsert', dest='minInsert', help='Minimum insert size for valid paired-end alignments') parser.add_option('', '--maxInsert', dest='maxInsert', help='Maximum insert size for valid paired-end alignments') @@ -45,7 +45,6 @@ parser.add_option('', '--reverseAlign', dest='reverseAlign', help='Whether or not to attempt to align the reverse-complement reference strand') parser.add_option('', '--phased', dest='phased', help='Whether or not it should alternate between using the forward and mirror indexes in a series of phases so that only half of the index is resident in memory at one time') parser.add_option('', '--offrate', dest='offrate', help='Override the offrate of the index to n') - parser.add_option('', '--mm', dest='mm', help='Whether or not to use memory-mapped I/O to load the index') parser.add_option('', '--seed', dest='seed', help='Seed for pseudo-random number generator') parser.add_option('', '--dbkey', dest='dbkey', help='') parser.add_option('', '--params', dest='params', help='Whether to use default or specified parameters') @@ -70,10 +69,10 @@ if options.genomeSource == 'history': # set up commands if options.index_settings =='index_pre_set': - indexing_cmds = '' + indexing_cmds = '--quiet' else: try: - indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s' % \ + indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s --quiet' % \ (('','--noauto')[options.iauto_b=='set'], ('','--packed')[options.ipacked=='packed'], ('','--bmax %s'%options.ibmax)[options.ibmax!='None' and options.ibmax>=1], @@ -88,7 +87,7 @@ ('','--cutoff %s'%options.icutoff)[int(options.icutoff)>0], ('','--oldpmap')[options.ioldpmap=='yes']) except ValueError: - indexing_cmds = '' + indexing_cmds = '--quiet' # make temp directory for placement of indices and copy reference file there tmp_dir = tempfile.gettempdir() @@ -97,7 +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 > /dev/null' % (tmp_dir, indexing_cmds, options.ref, options.ref) + cmd1 = 'cd %s; bowtie-build %s -f %s %s' % (tmp_dir, indexing_cmds, options.ref, options.ref) try: os.system(cmd1) except Exception, erf: @@ -106,11 +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 8' + aligning_cmds = '-p %s --quiet' % 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 %s %s -p 8' % \ + '%s %s %s %s %s %s %s %s %s %s %s %s -p %s --quiet' % \ (('','-s %s'%options.skip)[options.skip!='None'], ('','-u %s'%options.alignLimit)[int(options.alignLimit)>0], ('','-5 %s'%options.trimH)[int(options.trimH)>=0], @@ -128,7 +127,6 @@ ('','--norc')[options.reverseAlign=='noReverse'], ('','--maxbts %s'%options.maxBacktracks)[options.maxBacktracks!='None' and (options.mismatchSeed=='2' or options.mismatchSeed=='3')], ('','-y')[options.tryHard=='doTryHard'], - ('','--chunkmbs %s'%options.threadMem)[options.threadMem!='None' and int(options.threadMem)>=0], ('','-k %s'%options.valAlign)[options.valAlign!='None' and int(options.valAlign)>=0], ('','-a')[options.allValAligns=='doAllValAligns' and int(options.allValAligns)>=0], ('','-m %s'%options.suppressAlign)[int(options.suppressAlign)>=0], @@ -137,18 +135,18 @@ ('','-B %s'%options.offbase)[int(options.offbase)>=0], ('','-z %s'%options.phased)[options.phased!='None'], ('','-o %s'%options.offrate)[int(options.offrate)>=0], - ('','--mm')[options.mm=='doMm'], - ('','--seed %s'%options.seed)[int(options.seed)>=0]) + ('','--seed %s'%options.seed)[int(options.seed)>=0], + options.threads) except ValueError: - aligning_cmds = '-p 8' + aligning_cmds = '-p %s --quiet' % options.threads tmp_out = tempfile.NamedTemporaryFile() # prepare actual aligning commands if options.paired == 'paired': - cmd2 = 'bowtie %s %s -1 %s -2 %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.input1, options.input2, tmp_out.name) + cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % (aligning_cmds, options.ref, options.input1, options.input2, tmp_out.name) else: - cmd2 = 'bowtie %s %s %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.input1, tmp_out.name) + cmd2 = 'bowtie %s %s %s > %s' % (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) diff -r 7f4c8fee3b39 -r e58e140b89f7 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Mon Sep 14 12:23:16 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.xml Mon Sep 14 14:54:11 2009 -0400 @@ -2,6 +2,7 @@ <description> fast alignment of reads against reference sequence </description> <command interpreter="python"> bowtie_wrapper.py + --threads="8" --input1=$singlePaired.input1 #if $singlePaired.sPaired == "paired": --input2=$singlePaired.input2 @@ -33,17 +34,14 @@ --suppressAlign=$singlePaired.params.suppressAlign --offbase=$singlePaired.params.offbase --offrate=$singlePaired.params.offrate - --mm=$singlePaired.params.mm --seed=$singlePaired.params.seed --best=$singlePaired.params.bestOption.best #if $singlePaired.params.bestOption.best == "doBest": --maxBacktracks=$singlePaired.params.bestOption.maxBacktracks - --threadMem=$singlePaired.params.bestOption.threadMem --strata=$singlePaired.params.bestOption.strata --phased="None" #else: --maxBacktracks="None" - --threadMem="None" --strata="None" #if $singlePaired.sPaired =="single": --phased=$singlePaired.params.bestOption.phased @@ -83,7 +81,6 @@ --offbase="None" --best="None" --maxBacktracks="None" - --threadMem="None" --strata="None" --minInsert="None" --maxInsert="None" @@ -93,7 +90,6 @@ --reverseAlign="None" --phased="None" --offrate="None" - --mm="None" --seed="None" #end if #if $refGenomeSource.genomeSource == "history": @@ -264,7 +260,6 @@ </when> <when value="doBest"> <param name="maxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> - <param name="threadMem" type="integer" value="32" label="Number of megabytes of memory a given thread is given to store path descriptors in best mode (--chunkmbs)" help="If running in best mode, and you run out of memory, try adjusting this" /> <param name="strata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> <option value="noStrata">Do not use strata option</option> <option value="doStrata">Use strata option</option> @@ -272,10 +267,6 @@ </when> </conditional> <!-- bestOption --> <param name="offrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> - <param name="mm" type="select" label="Whether or not to use memory-mapped I/O to load the index (--m)"> - <option value="noMm">Use POSIX/C file I/O</option> - <option value="doMm">Use memory-mapped I/O</option> - </param> <param name="seed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> </when> <!-- full --> </conditional> <!-- params --> @@ -339,7 +330,6 @@ </when> <when value="doBest"> <param name="maxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> - <param name="threadMem" type="integer" value="32" label="Number of megabytes of memory a given thread is given to store path descriptors in best mode (--chunkmbs)" help="If running in best mode, and you run out of memory, try adjusting this" /> <param name="strata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> <option value="noStrata">Do not use strata option</option> <option value="doStrata">Use strata option</option> @@ -347,10 +337,6 @@ </when> </conditional> <param name="offrate" type="integer" value="-1" label="Override the offrate of the index to n -o)" help="-1 for default" /> - <param name="mm" type="select" label="Whether or not to use memory-mapped I/O to load the index (--mm)"> - <option value="noMm">Use POSIX/C file I/O</option> - <option value="doMm">Use memory-mapped I/O</option> - </param> <param name="seed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> </when> <!-- full --> </conditional> <!-- params --> @@ -431,10 +417,8 @@ <param name="offbase" value="0" /> <param name="best" value="doBest" /> <param name="maxBacktracks" value="800" /> - <param name="threadMem" value="32" /> <param name="strata" value="noStrata" /> <param name="offrate" value="-1" /> - <param name="mm" value="noMm" /> <param name="seed" value="403" /> <output name="output" ftype="sam" file="bowtie_out2.sam" /> </test>