comparison bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py @ 27:7b142d90bb06 draft

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26:7065bba6e7cd

                    snpfrac = '--snpfrac %s' % options.snpfrac
            if options.keepends and options.keepends == 'doKeepends':
                keepends = '--col-keepends'
            else:
                keepends = ''
            aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \
                            '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \
                            ( maxInsert, mateOrient, options.threads, suppressHeader,
                              colorspace, skip, alignLimit, trimH, trimL, maxMismatches,
                              mismatchSeed, mismatchQual, seedLen, rounding, minInsert,
                              maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks,

27:7b142d90bb06

                    snpfrac = '--snpfrac %s' % options.snpfrac
            if options.keepends and options.keepends == 'doKeepends':
                keepends = '--col-keepends'
            else:
                keepends = ''
            if options.output_unmapped_reads_l or options.output_unmapped_reads_r or options.output_unmapped_reads:
                aligning_cmds = '-q %s %s -p %s %s %s %s %s %s %s %s %s %s %s %s %s ' \
                            '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \
                            ( maxInsert, mateOrient, options.threads, suppressHeader,
                              colorspace, skip, alignLimit, trimH, trimL, maxMismatches,
                              mismatchSeed, mismatchQual, seedLen, rounding, minInsert,
                              maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks,
                              tryHard, valAlign, allValAligns, suppressAlign, best,
                              strata, offrate, seed, snpphred, snpfrac, keepends,
                              output_unmapped_reads, output_suppressed_reads,
                              quality_score_encoding )
            else:
                aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \
                            '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \
                            ( maxInsert, mateOrient, options.threads, suppressHeader,
                              colorspace, skip, alignLimit, trimH, trimL, maxMismatches,
                              mismatchSeed, mismatchQual, seedLen, rounding, minInsert,
                              maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks,