Mercurial > repos > jackcurragh > ribogalaxy_bowtie_rrna

comparison bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.py @ 5:b300c15426f5 draft

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Uploaded
author jackcurragh
date Mon, 21 Mar 2022 12:53:51 +0000
parents 9424721e6296
children 82854aad329b
comparison
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4:01ca7075c109 5:b300c15426f5
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' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
416 else: 416 else:
417 cmd2 = 'echo "bowtie %s %s %s > %s" > ~/galaxy_test.txt' % ( aligning_cmds, ref_file_name, options.input1, options.output ) 417 cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
418 # align 418 # align
419 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name 419 tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
420 with open(tmp, 'w') as tmp_stderr: 420 with open(tmp, 'w') as tmp_stderr:
421 returncode = subprocess.call(args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno()) 421 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 422 # get stderr, allowing for case where it's very large