Mercurial > repos > jackcurragh > ribogalaxy_bowtie_transcriptome
comparison bowtie_transcriptome_wrapper/bowtie_transcriptome_wrapper.py @ 8:f6ef1c85b045 draft
Uploaded
author | jackcurragh |
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date | Fri, 13 May 2022 09:53:29 +0000 |
parents | 14fb4b4872e3 |
children |
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7:d57209761277 | 8:f6ef1c85b045 |
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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 |