Python gZipEntropy Examples

Example #1

File: degOverview.py Project: sknyx/ResearchScripts

def updateGScore(oFN, rn=None, tn=None):

    oNX = cgNexusFlat.Nexus(oFN, degPeak.degPeak)
    oNX.load(['gScore', 'sequence'], [rn, tn])

    for oID in oNX.gScore:

        oNX.gScore[oID] = gZipEntropy.gZipEntropy(oNX.sequence[oID])

    oNX.save()

Example #2

File: updateGScore.py Project: JasonAng/ResearchScripts

def updateGScore(oFN, rn = None, tn = None):
        
        oNX = cgNexusFlat.Nexus(oFN, cgOriginRNAFlat.OriginRNA)
        oNX.load(['gScore', 'sequence'], [rn, tn])

        for oID in oNX.gScore:
                oNX.gScore[oID] = gZipEntropy.gZipEntropy(oNX.sequence[oID])


        oNX.save()

Example #3

File: updateDegPeaks.py Project: cgreer/ResearchScripts

def updateGScore(oFN, rn = None, tn = None):
        
        oNX = cgNexusFlat.Nexus(oFN, cgDegPeak.Peak)
        oNX.load(['gScore', 'gSequence'], [rn, tn])

        for oID in oNX.gScore:

                oNX.gScore[oID] = gZipEntropy.gZipEntropy(oNX.gSequence[oID])


        oNX.save()

Example #4

File: test.countDups.py Project: sknyx/ResearchScripts

def countDups(fN):

    f = open(fN, 'r')
    for line in f:
        ls = line.strip().split('\t')
        seq = ls[3]
        numDups = len(ls[2].split(','))
        numT = len(ls[9].split(','))
        rStatus = ls[21]
        gEnt = gz.gZipEntropy(seq)

        print '\t'.join([str(numDups), seq, str(numT), rStatus, gEnt])
    f.close()

Example #5

File: test.countDups.py Project: JasonAng/ResearchScripts

def countDups(fN):
        
        f = open(fN, 'r')
        for line in f:
                ls = line.strip().split('\t')
                seq = ls[3]
                numDups = len(ls[2].split(','))
                numT = len(ls[9].split(','))
                rStatus = ls[21]
                gEnt = gz.gZipEntropy(seq)

                print '\t'.join([str(numDups), seq, str(numT), rStatus, gEnt])
        f.close()