def simulateCounts(goInput, geneGoTerms, outFN, numSims = 1000):
#collect all terms
gName_goTerms = cgDictHelp.dictFromColumns(geneGoTerms, (0, 1), ('string', 'stringList'))
#collect data set
gName_backgroundSet = cgDictHelp.dictFromColumns(goInput, (0, 1), ('string', 'stringList'))
#collect unique go terms in data set
dataGoTerms = []
for gName in gName_backgroundSet:
dataGoTerms.extend(gName_goTerms[gName])
dataGoTerms = list(set(dataGoTerms))
#this will contain count for each sim performed
goTerm_simCounts = dict( (term, []) for term in dataGoTerms )
for i in range(1,numSims):
#init counts
goTerm_count = dict( (term, 0) for term in dataGoTerms)
pairedControl = []
for gName in gName_backgroundSet:
pairedControl.append(random.choice(gName_backgroundSet[gName]))
updateGoCounts(goTerm_count, gName_goTerms, pairedControl)
for goTerm, count in goTerm_count.items():
goTerm_simCounts[goTerm].append(count)
f = open(outFN, 'w')
for term in sorted(goTerm_simCounts.keys()):
f.write('%s\t%s\n' % (term, ','.join([str(x) for x in goTerm_simCounts[term]])) )
f.close()
def simulateCounts(goInput, geneGoTerms, outFN, numSims=1000):
#collect all terms
gName_goTerms = cgDictHelp.dictFromColumns(geneGoTerms, (0, 1),
('string', 'stringList'))
#collect data set
gName_backgroundSet = cgDictHelp.dictFromColumns(goInput, (0, 1),
('string', 'stringList'))
#collect unique go terms in data set
dataGoTerms = []
for gName in gName_backgroundSet:
dataGoTerms.extend(gName_goTerms[gName])
dataGoTerms = list(set(dataGoTerms))
#this will contain count for each sim performed
goTerm_simCounts = dict((term, []) for term in dataGoTerms)
for i in range(1, numSims):
#init counts
goTerm_count = dict((term, 0) for term in dataGoTerms)
pairedControl = []
for gName in gName_backgroundSet:
pairedControl.append(random.choice(gName_backgroundSet[gName]))
updateGoCounts(goTerm_count, gName_goTerms, pairedControl)
for goTerm, count in goTerm_count.items():
goTerm_simCounts[goTerm].append(count)
f = open(outFN, 'w')
for term in sorted(goTerm_simCounts.keys()):
f.write('%s\t%s\n' %
(term, ','.join([str(x) for x in goTerm_simCounts[term]])))
f.close()
def getPVals(goInput, simCountFN, geneGoTerms):
#load data
gName_goTerms = cgDictHelp.dictFromColumns(geneGoTerms, (0, 1), ('string', 'stringList'))
gName_backgroundSet = cgDictHelp.dictFromColumns(goInput, (0, 1), ('string', 'stringList'))
goTerm_simCounts = cgDictHelp.dictFromColumns(simCountFN, (0, 1), ('string', 'intList'))
#get data counts (observations)
goTerm_count = dict( (term, 0) for term in goTerm_simCounts )
updateGoCounts(goTerm_count, gName_goTerms, gName_backgroundSet.keys())
#get pVals
for goTerm, simCounts in goTerm_simCounts.iteritems():
actualObservation = goTerm_count[goTerm]
print '%s\t%s\t%s' % (goTerm, actualObservation, '\t'.join([str(x) for x in getPValInfo(actualObservation, simCounts)]))
def pickBackgroundGenes(goSet, geneSet, goInput, geneGoTerms):
NX = cgNexusFlat.Nexus(geneSet, geneProperty)
NX.load(['geneName', 'geneLength', 'geneGCContent'])
#inverse on gName
geneName_id = NX.iDictionary('geneName')
#gene go terms to filter genes that dont have go terms
gName_goTerms = cgDictHelp.dictFromColumns(geneGoTerms, (0, 1), ('string', 'stringList'))
#first get length, GC ranges for go set
usedGenes = []
gName__lRange__GCRange = []
f = open(goSet, 'r')
for line in f:
ls = line.strip().split('\t')
gName = ls[0]
usedGenes.append(gName)
if gName not in geneName_id:
print gName, 'not in dataset!'
continue
if gName not in gName_goTerms:
print gName, 'has no entry in go terms!'
continue
nID = geneName_id[gName]
gLength = NX.geneLength[nID]
gGC = NX.geneGCContent[nID]
gName__lRange__GCRange.append((gName, (gLength - .05*gLength, gLength + .05*gLength), (gGC - .05*gGC, gGC + .05*gGC)))
f.close()
#go through background set and pick acceptable genes
gName_bSet = {}
for gName, lRange, GCRange in gName__lRange__GCRange:
for id in NX.ids:
bGeneName = NX.geneName[id]
if bGeneName in usedGenes: continue
if bGeneName not in gName_goTerms: continue
theLength, theGC = NX.geneLength[id], NX.geneGCContent[id]
if (GCRange[0] <= theGC <= GCRange[1]) and (lRange[0] <= theLength <= lRange[1]):
gName_bSet.setdefault(gName, []).append(bGeneName)
#write it to background file
fOut = open(goInput, 'w')
for gName, bSet in gName_bSet.iteritems():
print gName, '# background genes', len(bSet)
outString = [gName]
outString.append(','.join(bSet))
outString = '\t'.join([str(x) for x in outString])
fOut.write(outString + '\n')
fOut.close()
def getPVals(goInput, simCountFN, geneGoTerms):
#load data
gName_goTerms = cgDictHelp.dictFromColumns(geneGoTerms, (0, 1),
('string', 'stringList'))
gName_backgroundSet = cgDictHelp.dictFromColumns(goInput, (0, 1),
('string', 'stringList'))
goTerm_simCounts = cgDictHelp.dictFromColumns(simCountFN, (0, 1),
('string', 'intList'))
#get data counts (observations)
goTerm_count = dict((term, 0) for term in goTerm_simCounts)
updateGoCounts(goTerm_count, gName_goTerms, gName_backgroundSet.keys())
#get pVals
for goTerm, simCounts in goTerm_simCounts.iteritems():
actualObservation = goTerm_count[goTerm]
print '%s\t%s\t%s' % (goTerm, actualObservation, '\t'.join(
[str(x) for x in getPValInfo(actualObservation, simCounts)]))
def pickBackgroundGenes(goSet, geneSet, goInput, geneGoTerms):
NX = cgNexusFlat.Nexus(geneSet, geneProperty)
NX.load(['geneName', 'geneLength', 'geneGCContent'])
#inverse on gName
geneName_id = NX.iDictionary('geneName')
#gene go terms to filter genes that dont have go terms
gName_goTerms = cgDictHelp.dictFromColumns(geneGoTerms, (0, 1),
('string', 'stringList'))
#first get length, GC ranges for go set
usedGenes = []
gName__lRange__GCRange = []
f = open(goSet, 'r')
for line in f:
ls = line.strip().split('\t')
gName = ls[0]
usedGenes.append(gName)
if gName not in geneName_id:
print gName, 'not in dataset!'
continue
if gName not in gName_goTerms:
print gName, 'has no entry in go terms!'
continue
nID = geneName_id[gName]
gLength = NX.geneLength[nID]
gGC = NX.geneGCContent[nID]
gName__lRange__GCRange.append(
(gName, (gLength - .05 * gLength, gLength + .05 * gLength),
(gGC - .05 * gGC, gGC + .05 * gGC)))
f.close()
#go through background set and pick acceptable genes
gName_bSet = {}
for gName, lRange, GCRange in gName__lRange__GCRange:
for id in NX.ids:
bGeneName = NX.geneName[id]
if bGeneName in usedGenes: continue
if bGeneName not in gName_goTerms: continue
theLength, theGC = NX.geneLength[id], NX.geneGCContent[id]
if (GCRange[0] <= theGC <= GCRange[1]) and (lRange[0] <= theLength
<= lRange[1]):
gName_bSet.setdefault(gName, []).append(bGeneName)
#write it to background file
fOut = open(goInput, 'w')
for gName, bSet in gName_bSet.iteritems():
print gName, '# background genes', len(bSet)
outString = [gName]
outString.append(','.join(bSet))
outString = '\t'.join([str(x) for x in outString])
fOut.write(outString + '\n')
fOut.close()