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Updated Bowtie wrapper tool to add a number of threads parameter and remove two unnecessary options

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This commit is contained in:
Kelly Vincent
2009-09-14 14:54:11 -04:00
parent f11dcd9781
commit f2aaa29988
2 changed files with 13 additions and 31 deletions
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tools/sr_mapping/bowtie_wrapper.py
+12 -14
View File
@@ -13,6 +13,7 @@ def stop_err( msg ):
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 @@ def __main__():
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 @@ def __main__():
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 @@ def __main__():
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 @@ def __main__():
('','--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 @@ def __main__():
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 @@ def __main__():
# 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 @@ def __main__():
('','--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 @@ def __main__():
('','-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)
tools/sr_mapping/bowtie_wrapper.xml
+1 -17
View File
@@ -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>