import bioLibCG import sys from parRun import parRun from checkExit import parClean import subprocess #fN and Init oFN = sys.argv[1] aFN = sys.argv[2] aFilteredFN = aFN #+ '.filtered' timer = bioLibCG.cgTimer() timer.start() #link oRNA to filteredTargets print 'linking oRNA to filtered targets' parRun(1, 'LOCAL', '/home/chrisgre/scripts/endoClip/siRnaPredictFlat.py', 'updateTargetIDsFiltered', oFN, aFilteredFN) #parClean(oFN, 30) print timer.split()
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() parRun(30, 3, '/home/chrisgre/scripts/alignSeqs/updateMismatchAndMiddleFlat.py', 'markMismatchedPairs', aFN) parClean(aFN, 30) print timer.split()
import bioLibCG import sys from parRun import parRun from checkExit import parClean import subprocess #fN and Init aFN = sys.argv[1] aFilteredFN = sys.argv[2] cLevel = sys.argv[3] timer = bioLibCG.cgTimer() timer.start() #filter targets print 'filtering targets' parRun(5, 3, '/home/chrisgre/scripts/endoClip/filteringFlat.py', 'filterTargetsInPlace', aFN, 'True', '1', '1', '.%s' % cLevel) parClean(aFN, 5) print timer.split() #make db smaller print 'truncating db' subprocess.Popen(['/home/chrisgre/scripts/endoClip/truncate.filterAlignments.sh', aFN, aFilteredFN]).wait() print timer.split()
import bioLibCG import sys from parRun import parRun from checkExit import parClean import subprocess import blankIDs #fN and Init oFN = sys.argv[1] aFN = sys.argv[2] aFilteredFN = aFN #+ '.filtered' seqFN = sys.argv[3] timer = bioLibCG.cgTimer() timer.start() #create oRNA file(simulated only) blankIDs.copyIDs(seqFN, oFN) #link oRNA to filteredTargets print 'linking oRNA to filtered targets' parRun(1, 'LOCAL', '/home/chrisgre/scripts/endoClip/siRnaPredictFlat.py', 'updateTargetIDsFiltered', oFN, aFilteredFN) #parClean(oFN, 30) print timer.split()
import sys import blankIDs from parRun import parRun from checkExit import parClean #files and init aFN = sys.argv[1] dFN = sys.argv[2] timer = bioLibCG.cgTimer() timer.start() #initializing alignments ''' print '...appending T Info' parRun(50, 3, '/home/chrisgre/myLibs/cgAlignmentFlat.py', 'appendTInfoFlat', aFN, dFN) parClean(aFN, 50) print timer.split() ''' print '...updating paired interactions: centered mismatches and center expression' parRun(40, 5, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markCenterExpression', aFN, '/home/chrisgre/smallLibs/siRNA/degradome/wigsk50') parClean(aFN, 40) print timer.split() ''' parRun(50, 3, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markMismatchedPairs', aFN) parClean(aFN, 50) print timer.split()
import bioLibCG import sys import blankIDs from parRun import parRun from checkExit import parClean #files and init aFN = sys.argv[1] dFN = sys.argv[2] timer = bioLibCG.cgTimer() timer.start() #initializing alignments ''' print '...appending T Info' parRun(50, 3, '/home/chrisgre/myLibs/cgAlignmentFlat.py', 'appendTInfoFlat', aFN, dFN) parClean(aFN, 50) print timer.split() ''' print '...updating paired interactions: centered mismatches and center expression' parRun(40, 5, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markCenterExpression', aFN, '/home/chrisgre/smallLibs/siRNA/degradome/wigsk50') parClean(aFN, 40) print timer.split() ''' parRun(50, 3, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markMismatchedPairs', aFN) parClean(aFN, 50) print timer.split()
import blankIDs from parRun import parRun from checkExit import parClean from checkExit import parCleanSplit from splitRun import splitRun #files and init aFN = sys.argv[1] dFN = sys.argv[2] timer = bioLibCG.cgTimer() timer.start() #initializing alignments print '...appending T Info' parRun(5, 3, '/home/chrisgre/myLibs/cgAlignmentFlat.py', 'appendTInfoFlat', aFN, dFN) parCleanSplit(aFN, 5) print timer.split() print '...updating paired interactions: center expression' #splitRun(aFN, 5, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markCenterExpression', 'splitFN', '/home/chrisgre/smallLibs/siRNA/degradome/wigsk50') #splitRun(aFN, 5, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markCenterExpression', 'splitFN', '/home/chrisgre/smallLibs/siRNA/degradome/HeLa/wigs.3t7n0m20k20b.contigFiltered') splitRun(aFN, 5, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markCenterExpression', 'splitFN', '/home/chrisgre/data/Lab_Data/U87/result_primary/wigs.n0m20k20b') parCleanSplit(aFN, 5) print timer.split() print '...updating paired interactions: center mismatch' splitRun(aFN, 3,
import bioLibCG import sys from parRun import parRun from checkExit import parClean import subprocess #fN and Init aFN = sys.argv[1] aFilteredFN = sys.argv[2] cLevel = sys.argv[3] timer = bioLibCG.cgTimer() timer.start() #filter targets print 'filtering targets' parRun(5, 3, '/home/chrisgre/scripts/endoClip/filteringFlat.py', 'filterTargetsInPlace', aFN, 'True', '1', '1', '.%s' % cLevel) parClean(aFN, 5) print timer.split() #make db smaller print 'truncating db' subprocess.Popen([ '/home/chrisgre/scripts/endoClip/truncate.filterAlignments.sh', aFN, aFilteredFN ]).wait() 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 blankIDs from parRun import parRun from checkExit import parClean from checkExit import parCleanSplit from splitRun import splitRun #files and init aFN = sys.argv[1] dFN = sys.argv[2] timer = bioLibCG.cgTimer() timer.start() #initializing alignments print '...appending T Info' parRun(5, 3, '/home/chrisgre/myLibs/cgAlignmentFlat.py', 'appendTInfoFlat', aFN, dFN) parCleanSplit(aFN, 5) print timer.split() print '...updating paired interactions: center expression' #splitRun(aFN, 5, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markCenterExpression', 'splitFN', '/home/chrisgre/smallLibs/siRNA/degradome/wigsk50') splitRun(aFN, 5, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markCenterExpression', 'splitFN', '/home/chrisgre/smallLibs/siRNA/degradome/Bracken/wigs/kidney') parCleanSplit(aFN, 5) print timer.split() print '...updating paired interactions: center mismatch' splitRun(aFN, 3, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markMismatchedPairs', 'splitFN') parClean(aFN, 5) print timer.split()
"""Also assumes that the results files have been made...""" oFN = runName + "/oRNA.data" aFN = runName + "/all.aligned.0.5.tabs" seqFN = runName + "/oRNA.sequences" tFN = runName + "/dRNA.results" timer = bioLibCG.cgTimer() timer.start() # initialize oRNA blankIDs.blankIDs(seqFN, oFN) # initializing alignments print "...appending T Info" parRun(40, 3, "/home/chrisgre/scripts/alignSeqs/cgAlignmentFlat.py", "appendTInfo", aFN, tFN) parClean(aFN, 40) print "...appending Tran Info" parRun(40, 3, "/home/chrisgre/scripts/alignSeqs/cgAlignmentFlat.py", "appendTranInfo", aFN, tFN) parClean(aFN, 40) print timer.split() print "...updating paired interactions: centered mismatches and center expression" parRun( 30, 4, "/home/chrisgre/scripts/alignSeqs/updateMismatchAndMiddleFlat.py", "markCenterExpression", aFN, "/home/chrisgre/smallLibs/siRNA/degradome/wigsk50",