def profileTargets(tccList, cName, dir=None, min=0): if not dir: dir = 'out' cg.clearDirectory(dir) #clear and/or make for tcc in tccList: plot.plotASProfile(tcc, cName, directory=dir, min=min)
def profileTargets(tccList, cName, dir = None, min = 0): if not dir: dir = 'out' cg.clearDirectory(dir) #clear and/or make for tcc in tccList: plot.plotASProfile(tcc, cName, directory = dir, min = min)
def writeWigFromHitDict(hitDict, assembly, name, directory=None): mConf = c.getConfig('Main.conf') if not directory: directory = mConf.conf['wigs'] if not name: name = cg.getBaseFileName(name, naked=True) lDict = cg.returnChromLengthDict(assembly) cg.clearDirectory(directory, overwrite=False) #write results to wig file for chrom in hitDict: for strand in hitDict[chrom]: oF = open(directory + '/%s.%s.%s.wig' % (name, chrom, strand), 'w') oF.write('track type=bedGraph name=%s.%s.%s\n' % (name, chrom, strand)) #print ' sorting' #print hitDict[chrom] chromEnd = lDict[chrom] # hitDict[chrom][strand][chromEnd] = 0 keys = hitDict[chrom][strand].keys() keys.sort() #print ' writing blocks' prevVal = 0 prevCoord = 0 blockStart = 0 blockEnd = 1 for key in keys: val = hitDict[chrom][strand][key] if prevCoord == key - 1: if val == prevVal: #should be combined blockEnd = key + 1 else: #no zero block #write old block oF.write('%s\t%s\t%s\t%s\n' % (chrom, blockStart, blockEnd, prevVal)) #!make it a float value? #start new block blockStart = key blockEnd = key + 1 else: #write old block oF.write('%s\t%s\t%s\t%s\n' % (chrom, blockStart, blockEnd, prevVal)) #write zero block oF.write('%s\t%s\t%s\t%s\n' % (chrom, blockEnd, key, 0)) #start new block blockStart = key blockEnd = key + 1 prevVal = val prevCoord = key oF.close()
def writeWigFromHitDict(hitDict, assembly, name, directory = None): mConf = c.getConfig('Main.conf') if not directory: directory = mConf.conf['wigs'] if not name: name = cg.getBaseFileName(name, naked = True) lDict = cg.returnChromLengthDict(assembly) cg.clearDirectory(directory, overwrite = False) #write results to wig file for chrom in hitDict: for strand in hitDict[chrom]: oF = open(directory + '/%s.%s.%s.wig' % (name, chrom, strand), 'w') oF.write('track type=bedGraph name=%s.%s.%s\n' % (name, chrom, strand)) #print ' sorting' #print hitDict[chrom] chromEnd = lDict[chrom] # hitDict[chrom][strand][chromEnd] = 0 keys = hitDict[chrom][strand].keys() keys.sort() #print ' writing blocks' prevVal = 0 prevCoord = 0 blockStart = 0 blockEnd = 1 for key in keys: val = hitDict[chrom][strand][key] if prevCoord == key - 1: if val == prevVal:#should be combined blockEnd = key + 1 else: #no zero block #write old block oF.write('%s\t%s\t%s\t%s\n' % (chrom, blockStart, blockEnd, prevVal)) #!make it a float value? #start new block blockStart = key blockEnd = key + 1 else: #write old block oF.write('%s\t%s\t%s\t%s\n' % (chrom, blockStart, blockEnd, prevVal)) #write zero block oF.write('%s\t%s\t%s\t%s\n' % (chrom, blockEnd, key, 0)) #start new block blockStart = key blockEnd = key + 1 prevVal = val prevCoord = key oF.close()
def plotResults(fN, cName=None): cHairs = getHairpins.getHairpins(fN) #CID: HAIRPIN directory = cg.getBaseFileName(fN) cg.clearDirectory(directory) #change the directory before plotting cwd = os.getcwd() os.chdir(directory) for CID in cHairs: print 'plotting:', CID cgPlot.plotASProfile(cHairs[CID], cName) os.chdir(cwd)
def plotResults(fN, cName = None): cHairs = getHairpins.getHairpins(fN) #CID: HAIRPIN directory = cg.getBaseFileName(fN) cg.clearDirectory(directory) #change the directory before plotting cwd = os.getcwd() os.chdir(directory) for CID in cHairs: print 'plotting:', CID cgPlot.plotASProfile(cHairs[CID], cName) os.chdir(cwd)