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In Bowtie wrapper tool, removed --quiet option and redirected stderr to /dev/null

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This commit is contained in:
Kelly Vincent
2009-09-15 14:26:20 -04:00
parent 2abf463a95
commit db273d3c2d
1 changed files with 9 additions and 9 deletions
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tools/sr_mapping/bowtie_wrapper.py
+9 -9
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@@ -69,10 +69,10 @@ def __main__():
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 @@ def __main__():
('','--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 @@ 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' % (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 @@ 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 %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 @@ def __main__():
('','--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)