import siRnaPredict import cgSort ''' si.predictSiRNA('small.peak.data', 'siDegradome.conf') si.updateSmallExpression('small.degradome', 'siPeaks.conf') si.exonOverlap('small.degradome.small') ''' ''' cgSort.sortFileCG('small.degradome.small.degOverlap', 1, rev = True) cgSort.sortFileCG('small.degradome.small.degOverlap', 2, rev = True) ''' ''' f = open('/home/chrisgre/smallLibs/siRNA/small/SRR029124.fastq.clipped.mapped', 'r') for i in range(0,100): r = f.readline() print r read = siRnaPredict.readInfo(r) print read.chrom, read.strand, read.start, read.end print read.scores, read.mismatches print read.returnMismatchPositions() ''' directory = '/home/chrisgre/smallLibs/siRNA/small/sortedChroms' siRnaPredict.markMismatches('small.degradome.small.degOverlap.clean', directory)
import siRnaPredict import cgSort ''' si.predictSiRNA('small.peak.data', 'siDegradome.conf') si.updateSmallExpression('small.degradome', 'siPeaks.conf') si.exonOverlap('small.degradome.small') ''' ''' cgSort.sortFileCG('small.degradome.small.degOverlap', 1, rev = True) cgSort.sortFileCG('small.degradome.small.degOverlap', 2, rev = True) ''' ''' f = open('/home/chrisgre/smallLibs/siRNA/small/SRR029124.fastq.clipped.mapped', 'r') for i in range(0,100): r = f.readline() print r read = siRnaPredict.readInfo(r) print read.chrom, read.strand, read.start, read.end print read.scores, read.mismatches print read.returnMismatchPositions() ''' directory = '/home/chrisgre/smallLibs/siRNA/small/sortedChroms' siRnaPredict.markMismatches('small.degradome.small.degOverlap.clean', directory)
import siRnaPredict as si import cleanup import subprocess peakFName = 'small.peak.data' smallUpdateFN = 'small.degradome' cleanFN = 'small.degradome.small' exonUpdateFN = 'small.degradome.small.clean' mismatchFN = 'small.degradome.small.clean.degOverlap' clean2FN = 'small.degradome.small.clean.degOverlap.mismatch' sortFN = 'small.degradome.small.clean.degOverlap.mismatch.clean' smallDirectory = '/home/chrisgre/smallLibs/siRNA/small/sortedChroms' print 'Getting highest level, offset, middle level' si.predictSiRNA(peakFName, 'siDegradome.conf') print 'Getting small expression level' si.updateSmallExpression(smallUpdateFN, 'siPeaks.conf') print 'cleaning' cleanup.cleanup(cleanFN) print 'Getting transcript level' si.exonOverlap(exonUpdateFN) print 'Getting mismatch levels' si.markMismatches(mismatchFN, smallDirectory) print 'Cleaning up again, and sorting' cleanup.cleanup2(clean2FN) subprocess.Popen(['./sortIt.sh', sortFN], stdout=subprocess.PIPE, stderr=subprocess.PIPE)