alignTrunFN = runName + '.all.aligned.nodups' + '.' + str(minMismatches) + '.' + str(maxMismatches) sFN = runName + '.small.results' tFN = runName + '.degradome.results' #Get expression of the small RNAs and the targets print 'updating expression levels' #si.updateSmallExpression(sFN, 'siPeaks.conf', 1, 3, sFN) #si.updateSmallExpression(tFN, 'siDegradome.conf', 1, 2, tFN) print 'truncating alignments' #Truncate alignment file for specified mismatches si.truncateAlignments(alignFN, minMismatches, maxMismatches, alignTrunFN) print 'updating initial targets' #update the initial targets for small rnas based off of only local alignment si.updateTargetIDs(sFN, alignTrunFN, 0, 4, sFN) print 'update microrna/transcript overlaps' #update microRNA biogenesis for small and transcript #si.updateMicroRNAOverlap(sFN, 'mirBaseHumanNew.gff.Tcc', 1, 5, sFN) #si.transcriptSetOverlap(sFN, False, 1, 6, sFN) #si.transcriptSetOverlap(tFN, True, 1, 3, tFN) print 'updating paired interactions: centered mismatches and center expression' mm.markCenterExpression(sFN, tFN, alignTrunFN, 'siDegradome.conf', runName + '.pair.center.data') mm.markMismatchedPairs(sFN, alignTrunFN, runName + '.pair.mismatch.data')
seqFN = runName + '/oRNA.simSeqs' tFN = '/home/chrisgre/scripts/alignSeqs/dRNA.results.updated' timer = bioLibCG.cgTimer() timer.start() #initialize oRNA database print 'initializing oRNA' si.updateIDFromQuery(oRNADir, seqFN) print timer.split() #initializing alignments print 'Initializing alignments' print '...loading alignments' cgAlignment.loadAlignments2(aDir, alignTrunFN) 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') mm.markMismatchedPairs(aDir) print timer.split() print 'Linking oRNA to Targets' #update the initial targets for small rnas based off of only local alignment si.updateTargetIDs(oRNADir, aDir) print timer.split(), 'done', runName
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') mm.markMismatchedPairs(aDir) print timer.split() print 'Linking oRNA to Targets' #update the initial targets for small rnas based off of only local alignment si.updateTargetIDs(oRNADir, aDir) print timer.split() print 'DONE with', runName
