'''Pipeline assumes that full alignment of small to target seqs has been done, but not truncated''' '''Also assumes that the results files have been made...''' oRNADir = runName + '/oRNATest' aDir = runName + '/aDir' alignTrunFN = runName + '/all.aligned.0.5.filtered' seqFN = '/home/chrisgre/scripts/alignSeqs/oRNA.sequences' tFN = '/home/chrisgre/scripts/alignSeqs/dRNA.results.updated' timer = bioLibCG.cgTimer() timer.start() #initialize oRNA database print 'initializing oRNA' si.updateID(oRNADir, seqFN) print timer.split() #initializing alignments print 'Initializing alignments' print '...loading alignments' cgAlignment.loadAlignments2(aDir, alignTrunFN) print timer.split() print '...appending T Info' cgAlignment.appendTInfo(aDir, tFN) print '...appending Tran Info' cgAlignment.appendTranInfo(aDir, tFN) print timer.split() print '...updating paired interactions: centered mismatches and center expression'
aDir = runName + '/aDir' minMismatches = 0 maxMismatches = 5 alignFN = runName + '/all.aligned' alignTrunFN = runName + '/all.aligned' + '.' + str(minMismatches) + '.' + str(maxMismatches) peakFN = 'oRNA.results' tFN = 'dRNA.results.e.t' timer = bioLibCG.cgTimer() timer.start() #initialize oRNA database print 'initializing oRNA' si.updateID(oRNADir, peakFN) print timer.split() print 'truncating alignments' #Truncate alignment file for specified mismatches #si.truncateAlignments(alignFN, minMismatches, maxMismatches, alignTrunFN) print 'loading alignments' #initialize alignments #cgAlignment.loadAlignments2(aDir, alignTrunFN) #cgAlignment.appendTInfo(aDir, tFN) #cgAlignment.appendTranInfo(aDir, tFN) print timer.split() print 'updating initial targets' #update the initial targets for small rnas based off of only local alignment
runName = sys.argv[1] '''Pipeline assumes that full alignment of small to target seqs has been done, but not truncated''' '''Also assumes that the results files have been made...''' oRNADir = runName + '/oRNATest' aDir = runName + '/aDir' alignTrunFN = runName + '/all.aligned.0.5.filtered' seqFN = '/home/chrisgre/scripts/alignSeqs/oRNA.sequences' tFN = '/home/chrisgre/scripts/alignSeqs/dRNA.results.updated' timer = bioLibCG.cgTimer() timer.start() #initialize oRNA database print 'initializing oRNA' si.updateID(oRNADir, seqFN) print timer.split() #initializing alignments print 'Initializing alignments' print '...loading alignments' cgAlignment.loadAlignments2(aDir, alignTrunFN) print timer.split() print '...appending T Info' cgAlignment.appendTInfo(aDir, tFN) print '...appending Tran Info' cgAlignment.appendTranInfo(aDir, tFN) print timer.split() print '...updating paired interactions: centered mismatches and center expression' mm.markCenterExpression(aDir, 'siDegradome.conf')
