Mercurial > repos > jackcurragh > ribogalaxy_bowtie_rrna
comparison bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.py @ 5:b300c15426f5 draft
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author | jackcurragh |
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date | Mon, 21 Mar 2022 12:53:51 +0000 |
parents | 9424721e6296 |
children | 82854aad329b |
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4:01ca7075c109 | 5:b300c15426f5 |
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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 |