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Tophat wrapper improvements: (a) from JJ and Ry4an Brase @ UMN: wire up parameters from wrapper to tool and (b) improve path joining.

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This commit is contained in:
Jeremy Goecks
2010-10-27 18:14:18 -04:00
parent acbc070a66
commit c2e2c890c3
1 changed files with 12 additions and 6 deletions
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tools/ngs_rna/tophat_wrapper.py
+12 -6
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@@ -52,8 +52,6 @@ def __main__():
(options, args) = parser.parse_args()
#sys.stderr.write('*'*50+'\n'+str(options)+'\n'+'*'*50+'\n')
# Creat bowtie index if necessary.
tmp_index_dir = tempfile.mkdtemp()
if options.own_file != 'None':
@@ -121,6 +119,14 @@ def __main__():
opts += ' --microexon-search'
if options.single_paired == 'paired':
opts += ' --mate-std-dev %s' % options.mate_std_dev
if options.seg_mismatches != None:
opts += ' --segment-mismatches %d' % int(options.seg_mismatches)
if options.seg_length != None:
opts += ' --segment-length %d' % int(options.seg_length)
if options.min_segment_intron != None:
opts += ' --min-segment-intron %d' % int(options.min_segment_intron)
if options.max_segment_intron != None:
opts += ' --max-segment-intron %d' % int(options.max_segment_intron)
cmd = cmd % ( tmp_output_dir, opts, index_path, reads )
except Exception, e:
# Clean up temp dirs
@@ -166,12 +172,12 @@ def __main__():
# Postprocessing: copy output files from tmp directory to specified files. Also need to remove header lines from SAM file.
try:
try:
shutil.copyfile( tmp_output_dir + "/coverage.wig", options.coverage_output_file )
shutil.copyfile( tmp_output_dir + "/junctions.bed", options.junctions_output_file )
shutil.copyfile( os.path.join( tmp_output_dir, "coverage.wig" ), options.coverage_output_file )
shutil.copyfile( os.path.join( tmp_output_dir, "junctions.bed" ), options.junctions_output_file )
# Remove headers from SAM file in place.
in_header = True # Headers always at start of file.
for line in fileinput.input( tmp_output_dir + "/accepted_hits.sam", inplace=1 ):
for line in fileinput.input( os.path.join( tmp_output_dir, "accepted_hits.sam" ), inplace=1 ):
if in_header and line.startswith("@"):
continue
else:
@@ -179,7 +185,7 @@ def __main__():
sys.stdout.write( line )
# Copy SAM File.
shutil.copyfile( tmp_output_dir + "/accepted_hits.sam", options.accepted_hits_output_file )
shutil.copyfile( os.path.join( tmp_output_dir, "accepted_hits.sam" ), options.accepted_hits_output_file )
except Exception, e:
stop_err( 'Error in tophat:\n' + str( e ) )
finally: