def makeGraph(baseName, lowRange, highRange):
lowRange = int(lowRange)
highRange = int(highRange)
histDict = {}
for i in range(lowRange, highRange + 1):
f = open(baseName + str(i), 'r')
for line in f:
targets = line.strip().split('\t')[4]
numTargets = len(targets.split(','))
try:
histDict[i].append(numTargets)
except KeyError:
histDict[i] = [numTargets]
f.close()
print histDict
for m in histDict:
cgPlot.plotHistogram(histDict[m], name = str(m) + ' mismatches')
def makeFigure(fN, targetFN, alignmentFN, cName):
#make targetDict
f = open(targetFN, 'r')
targetDict = {} # tID: tLoc
for line in f:
ls = line.strip().split('\t')
targetDict[int(ls[0])] = ls[1]
f.close()
#make alignmentDict
alignDict = {} # sid: {target: offset}
f = open(alignmentFN, 'r')
for line in f:
ls = line.strip().split(' ')
sID = int(ls[0])
tID = int(ls[1])
offset = int(ls[4])
if not sID in alignDict:
alignDict[sID] = {}
alignDict[sID][tID] = offset #assumes one source to target...
f.close()
f = open(fN, 'r')
histoVals = []
for line in f:
ls = line.strip().split('\t')
sID = int(ls[0])
sLoc = ls[1]
sChrom, sStrand, sStart, sEnd = bioLibCG.tccSplit(sLoc)
sLen = sEnd - sStart
tIDs = ls[4].split(',')
for tID in tIDs:
tID = int(tID)
tLoc = targetDict[tID]
chrom, strand, start, end = bioLibCG.tccSplit(tLoc)
offset = alignDict[sID][tID]
if sStrand == '1':
start = start - 19 + offset
end = start + sLen
else:
end = end + 19 - offset
start = end - sLen
scanRange = bioLibCG.makeTcc(chrom, strand, start, end)
stretch = cgPeaks.stretch(scanRange, cName)
highest = stretch.getHighestLevel()
sortedKeys = stretch.profile.keys()
if sStrand == '-1':
sortedKeys.reverse()
i = 0
for key in sortedKeys:
level = stretch.profile[key]
for j in range(0,level):
histoVals.append(i)
i += 1
cgPlot.plotHistogram(histoVals)
tcc = 'chr1:1:1102538:1103319' stretch = cgPeaks.stretch(tcc, 'agoProfile.conf') stretch.createContBlocks() sortedKeys = stretch.profile.keys() sortedKeys.sort() for key in sortedKeys: print key, stretch.profile[key] for block in stretch.blocks: print block ''' ''' #histogram test a = [5,5,5,5,5,5,4,4,4,3,3,2,1] cgPlot.plotHistogram(a, name = 'testHistogram') ''' #svCoord test tcc = 'chr1:1:1103298:1103298' eLevels = sv.svCoord([tcc], 'siPeaks.conf') for coord in eLevels: print coord, eLevels[coord] ''' tcc = 'chr1:1:1102539:1103319'
import cgPlot
import bioLibCG as cg
f = open('cb.20.ago', 'r')
lengths = []
for line in f:
lengths.append(cg.getTccLength(line.strip()))
cgPlot.plotHistogram(lengths, name = 'cbLengths20')
def makeFigure(fN, targetFN, alignmentFN, cName):
# make targetDict
f = open(targetFN, "r")
targetDict = {} # tID: tLoc
for line in f:
ls = line.strip().split("\t")
targetDict[int(ls[0])] = ls[1]
f.close()
# make alignmentDict
alignDict = {} # sid: {target: offset}
f = open(alignmentFN, "r")
for line in f:
ls = line.strip().split(" ")
sID = int(ls[0])
tID = int(ls[1])
offset = int(ls[4])
if not sID in alignDict:
alignDict[sID] = {}
alignDict[sID][tID] = offset # assumes one source to target...
f.close()
f = open(fN, "r")
histoVals = []
for line in f:
ls = line.strip().split("\t")
sID = int(ls[0])
sLoc = ls[1]
sChrom, sStrand, sStart, sEnd = bioLibCG.tccSplit(sLoc)
sLen = sEnd - sStart
tIDs = ls[4].split(",")
for tID in tIDs:
tID = int(tID)
tLoc = targetDict[tID]
chrom, strand, start, end = bioLibCG.tccSplit(tLoc)
offset = alignDict[sID][tID]
if sStrand == "1":
start = start - 19 + offset
end = start + sLen
else:
end = end + 19 - offset
start = end - sLen
scanRange = bioLibCG.makeTcc(chrom, strand, start, end)
stretch = cgPeaks.stretch(scanRange, cName)
highest = stretch.getHighestLevel()
sortedKeys = stretch.profile.keys()
if sStrand == "-1":
sortedKeys.reverse()
i = 0
for key in sortedKeys:
level = stretch.profile[key]
for j in range(0, level):
histoVals.append(i)
i += 1
cgPlot.plotHistogram(histoVals)
import cgPlot
import bioLibCG as cg
f = open('cb.20.ago', 'r')
lengths = []
for line in f:
lengths.append(cg.getTccLength(line.strip()))
cgPlot.plotHistogram(lengths, name='cbLengths20')