Mercurial > repos > jackcurragh > ribogalaxy_bowtie_rrna

comparison bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py @ 22:ca7c965f7cc9 draft

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Uploaded
author jackcurragh
date Thu, 12 May 2022 14:15:48 +0000
parents b49ad9f12dfa
children 7b142d90bb06
comparison
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21:b49ad9f12dfa 22:ca7c965f7cc9
412 try: 412 try:
413 # prepare actual mapping commands 413 # prepare actual mapping commands
414 if options.output != 'XXXX': 414 if options.output != 'XXXX':
415 print('incorrect option') 415 print('incorrect option')
416 if options.paired == 'paired': 416 if options.paired == 'paired':
417 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 ) 417 # 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 )
418 else: 418 cmd2 = 'bowtie %s %s -1 %s -2 %s > %s ' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
419 cmd2 = 'bowtie %s %s %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output, options.output ) 419
420 else:
421 # cmd2 = 'bowtie %s %s %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output, options.output )
422 cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
423
420 else: 424 else:
421 if options.paired == 'paired': 425 if options.paired == 'paired':
422 cmd2 = 'bowtie %s %s -1 %s -2 %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2 ) 426 cmd2 = 'bowtie %s %s -1 %s -2 %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2 )
423 else: 427 else:
424 print('correct option') 428 print('correct option')