Mercurial > repos > jackcurragh > ribogalaxy_bowtie_rrna

comparison bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py @ 28:44e61af3637d draft

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Uploaded
author jackcurragh
date Tue, 12 Jul 2022 13:31:22 +0000
parents 7b142d90bb06
children 104d6756bcbc
comparison
equal deleted inserted replaced
27:7b142d90bb06 28:44e61af3637d
392 keepends = '--col-keepends' 392 keepends = '--col-keepends'
393 else: 393 else:
394 keepends = '' 394 keepends = ''
395 if options.output_unmapped_reads_l or options.output_unmapped_reads_r or options.output_unmapped_reads: 395 if options.output_unmapped_reads_l or options.output_unmapped_reads_r or options.output_unmapped_reads:
396 aligning_cmds = '-q %s %s -p %s %s %s %s %s %s %s %s %s %s %s %s %s ' \ 396 aligning_cmds = '-q %s %s -p %s %s %s %s %s %s %s %s %s %s %s %s %s ' \
397 '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \ 397 '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s --suppress' % \
398 ( maxInsert, mateOrient, options.threads, suppressHeader, 398 ( maxInsert, mateOrient, options.threads, suppressHeader,
399 colorspace, skip, alignLimit, trimH, trimL, maxMismatches, 399 colorspace, skip, alignLimit, trimH, trimL, maxMismatches,
400 mismatchSeed, mismatchQual, seedLen, rounding, minInsert, 400 mismatchSeed, mismatchQual, seedLen, rounding, minInsert,
401 maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks, 401 maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks,
402 tryHard, valAlign, allValAligns, suppressAlign, best, 402 tryHard, valAlign, allValAligns, suppressAlign, best,