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Corrected sloppy temp file/directory cleanup in index creation for Bowtie and BWA

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This commit is contained in:
Kelly Vincent
2009-11-12 13:02:04 -05:00
parent d2102123d9
commit 803cbc5ef4
2 changed files with 22 additions and 21 deletions
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tools/sr_mapping/bowtie_wrapper.py
+11 -13
View File
@@ -4,7 +4,7 @@
Runs Bowtie on single-end or paired-end data.
"""
import optparse, os, sys, tempfile
import optparse, os, shutil, sys, tempfile
def stop_err( msg ):
sys.stderr.write( "%s\n" % msg )
@@ -62,7 +62,8 @@ def __main__():
parser.add_option('', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set')
parser.add_option('', '--suppressHeader', dest='suppressHeader', help='Suppress header')
(options, args) = parser.parse_args()
# make temp directory for placement of indices and copy reference file there if necessary
tmp_index_dir = tempfile.mkdtemp()
# index if necessary
if options.genomeSource == 'history':
# set up commands
@@ -85,22 +86,19 @@ def __main__():
('','--cutoff %s'%options.icutoff)[int(options.icutoff)>0])
except ValueError:
indexing_cmds = ''
# make temp directory for placement of indices and copy reference file there
tmp_dir = tempfile.gettempdir()
try:
os.system('cp %s %s' % (options.ref, tmp_dir))
shutil.copy(options.ref, tmp_index_dir)
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 2> /dev/null' % (tmp_dir, indexing_cmds, options.ref, options.ref)
options.ref = os.path.join(tmp_index_dir,os.path.split(options.ref)[1])
cmd1 = 'bowtie-build %s -f %s %s 2> /dev/null' % (indexing_cmds, options.ref, options.ref)
try:
os.chdir(tmp_index_dir)
os.system(cmd1)
except Exception, erf:
stop_err('Error indexing reference sequence\n' + str(erf))
# set up aligning and generate aligning command options
# automatically set threads to 8 in both cases
# automatically set threads in both cases
if options.params == 'pre_set':
aligning_cmds = '-p %s -S' % options.threads
else:
@@ -134,19 +132,16 @@ def __main__():
options.threads)
except ValueError, erf:
stop_err('Something is wrong with the alignment parameters and the alignment could not be run\n' + str(erf))
# 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, options.output)
else:
cmd2 = 'bowtie %s %s %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.input1, options.output)
# align
try:
os.system(cmd2)
except Exception, erf:
stop_err("Error aligning sequence\n" + str(erf))
# remove header if necessary
if options.suppressHeader == 'true':
tmp_out = tempfile.NamedTemporaryFile()
@@ -171,5 +166,8 @@ def __main__():
line = output.readline()
fout.close()
tmp_out.close()
# clean up temp dir
if os.path.exists(tmp_index_dir):
shutil.rmtree(tmp_index_dir)
if __name__=="__main__": __main__()
tools/sr_mapping/bwa_wrapper.py
+11 -8
View File
@@ -5,7 +5,7 @@ Runs BWA on single-end or paired-end data.
Produces a SAM file containing the mappings.
"""
import optparse, os, sys, tempfile
import optparse, os, shutil, sys, tempfile
def stop_err( msg ):
sys.stderr.write( "%s\n" % msg )
@@ -43,13 +43,12 @@ def __main__():
parser.add_option('', '--dbkey', dest='dbkey', help='')
parser.add_option('', '--suppressHeader', dest='suppressHeader', help='Suppress header')
(options, args) = parser.parse_args()
# make temp directory for placement of indices and copy reference file there
tmp_index_dir = tempfile.mkdtemp()
# index if necessary
if options.fileSource == 'history':
# make temp directory for placement of indices and copy reference file there
tmp_dir = tempfile.gettempdir()
try:
os.system('cp %s %s' % (options.ref, tmp_dir))
shutil.copy(options.ref, tmp_index_dir)
except Exception, erf:
stop_err('Error creating temp directory for indexing purposes\n' + str(erf))
try:
@@ -64,9 +63,10 @@ def __main__():
indexing_cmds = '-c -a %s' % indexingAlg
else:
indexing_cmds = '-a %s' % indexingAlg
options.ref = os.path.join(tmp_dir,os.path.split(options.ref)[1])
cmd1 = 'cd %s; bwa index %s %s 2> /dev/null' % (tmp_dir, indexing_cmds, options.ref)
options.ref = os.path.join(tmp_index_dir,os.path.split(options.ref)[1])
cmd1 = 'bwa index %s %s 2> /dev/null' % (indexing_cmds, options.ref)
try:
os.chdir(tmp_index_dir)
os.system(cmd1)
except Exception, erf:
stop_err('Error indexing reference sequence\n' + str(erf))
@@ -89,10 +89,10 @@ def __main__():
gen_alignment_cmds = '-n %s' % options.outputTopN
elif options.genAlignType == 'paired':
gen_alignment_cmds = '-a %s -o %s' % (options.maxInsertSize, options.maxOccurPairing)
# print 'options.genAlignType: %s and commands: %s' % (options.genAlignType, gen_alignment_cmds)
# set up output files
tmp_align_out = tempfile.NamedTemporaryFile()
tmp_align_out2 = tempfile.NamedTemporaryFile()
# prepare actual aligning and generate aligning commands
cmd2 = 'bwa aln %s %s %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.fastq, tmp_align_out.name)
cmd2b = ''
@@ -144,5 +144,8 @@ def __main__():
line = output.readline()
fout.close()
tmp_out.close()
# clean up temp dir
if os.path.exists(tmp_index_dir):
shutil.rmtree(tmp_index_dir)
if __name__=="__main__": __main__()