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)