Mercurial > repos > jackcurragh > ribogalaxy_bowtie_transcriptome

comparison bowtie_transcriptome_wrapper/bowtie_transcriptome_wrapper.py @ 8:f6ef1c85b045 draft

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author jackcurragh
date Fri, 13 May 2022 09:53:29 +0000
parents 14fb4b4872e3
children
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7:d57209761277 8:f6ef1c85b045
410 try: 410 try:
411 # have to nest try-except in try-finally to handle 2.4 411 # have to nest try-except in try-finally to handle 2.4
412 try: 412 try:
413 # prepare actual mapping commands 413 # prepare actual mapping commands
414 if options.paired == 'paired': 414 if options.paired == 'paired':
415 cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output ) 415 # cmd2 = 'bowtie %s %s -1 %s -2 %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output, options.output )
416 else: 416 cmd2 = 'bowtie %s %s -1 %s -2 %s > %s ' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
417 cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output ) 417
418 else:
419 # cmd2 = 'bowtie %s %s %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output, options.output )
420 cmd2 = 'bowtie %s %s %s > %s ' % ( aligning_cmds, ref_file_name, options.input1, options.output )
421
418 # align 422 # align
419 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name 423 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
420 with open(tmp, 'w') as tmp_stderr: 424 with open(tmp, 'w') as tmp_stderr:
421 returncode = subprocess.call(args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno()) 425 returncode = subprocess.call(args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno())
422 # get stderr, allowing for case where it's very large 426 # get stderr, allowing for case where it's very large