from checkExit import parClean #files and init oFN = sys.argv[1] aFN = sys.argv[2] seqFN = sys.argv[3] tFN = '/home/chrisgre/scripts/alignSeqs/dRNA.results.updated' timer = bioLibCG.cgTimer() timer.start() #initialize oRNA blankIDs.blankIDs(seqFN, oFN) #initializing alignments print '...appending T Info' parRun(30, 3, '/home/chrisgre/scripts/alignSeqs/cgAlignmentFlat.py', 'appendTInfo', aFN, tFN) parClean(aFN, 30) print '...appending Tran Info' parRun(30, 3, '/home/chrisgre/scripts/alignSeqs/cgAlignmentFlat.py', 'appendTranInfo', aFN, tFN) parClean(aFN, 30) print timer.split() print '...updating paired interactions: centered mismatches and center expression' parRun(30, 5, '/home/chrisgre/scripts/alignSeqs/updateMismatchAndMiddleFlat.py', 'markCenterExpression', aFN, '/home/chrisgre/smallLibs/siRNA/degradome/wigsk50') parClean(aFN, 30) print timer.split()
import updateDegPeaks as degPeaks import sys import blankIDs from parRun import parRun from checkExit import parClean dRNAFN = sys.argv[1] peakFN = sys.argv[2] seqFN = sys.argv[3] timer = bioLibCG.cgTimer() timer.start() #initialize oRNA database print 'make blank IDs' blankIDs.blankIDs(seqFN, dRNAFN) print 'sequence' degPeaks.updateSequence(dRNAFN, seqFN) print 'tcc' degPeaks.updateTcc(dRNAFN, peakFN) print 'eLevel' degPeaks.updateELevel(dRNAFN, '/home/chrisgre/smallLibs/siRNA/degradome/wigsk50') print 'gSequence' degPeaks.updateGSequence(dRNAFN) print 'gScore' parRun(50, 3, '/home/chrisgre/scripts/endoClip/updateDegPeaks.py', 'updateGScore', dRNAFN) parClean(dRNAFN, 50)
import updateContigsFlat import updateDuplicatesMultiTcc as udmt import blankIDs oRNAFN = sys.argv[1] peakFN = sys.argv[2] seqFN = sys.argv[3] smallWigFN = sys.argv[4] timer = bioLibCG.cgTimer() timer.start() #initialize oRNA database print 'make blank IDs' blankIDs.blankIDs(seqFN, oRNAFN) print 'sequence' si.updateSequence(oRNAFN, seqFN) print 'tcc' si.updateTcc(oRNAFN, peakFN) print 'entropy' si.updateEntropy(oRNAFN) #si.updateELevel(oRNAFN, '/home/chrisgre/smallLibs/siRNA/small/wigsk50') si.updateELevel(oRNAFN, smallWigFN) print 'contigs' updateContigsFlat.updateTotalContig(oRNAFN) updateContigsFlat.updateEndContig(oRNAFN) print 'duplicates and mutlitcc' udmt.updateSeqDuplicateMultiTcc(oRNAFN) print timer.split()
import sys import updateContigsFlat import updateDuplicatesMultiTcc as udmt import blankIDs oRNAFN = sys.argv[1] peakFN = sys.argv[2] seqFN = sys.argv[3] smallWigFN = sys.argv[4] timer = bioLibCG.cgTimer() timer.start() #initialize oRNA database print 'make blank IDs' blankIDs.blankIDs(seqFN, oRNAFN) print 'sequence' si.updateSequence(oRNAFN, seqFN) print 'tcc' si.updateTcc(oRNAFN, peakFN) print 'entropy' si.updateEntropy(oRNAFN) #si.updateELevel(oRNAFN, '/home/chrisgre/smallLibs/siRNA/small/wigsk50') si.updateELevel(oRNAFN, smallWigFN) print 'contigs' updateContigsFlat.updateTotalContig(oRNAFN) updateContigsFlat.updateEndContig(oRNAFN) print 'duplicates and mutlitcc' udmt.updateSeqDuplicateMultiTcc(oRNAFN) print timer.split()