def addUTR(self,filename,genes):
hash=self.hashGenes(genes)
reader=BedReader(filename)
while(True):
record=reader.nextRecord()
if(not record): break
if(not record.isBed6()):
raise Exception("BED file has too few fields")
id=record.name
gene=hash.get(id,None)
if(not gene):
gene=BedGene(id,record.chr,record.strand)
genes.append(gene)
hash[id]=gene
gene.addUTR(record.interval)
for gene in genes:
gene.coalesce()
def readCDS(self, filename):
reader = BedReader(filename)
genes = []
genesByName = {}
while (True):
record = reader.nextRecord()
if (not record): break
if (not record.isBed6()):
raise Exception("BED file has too few fields")
id = record.name
gene = genesByName.get(id, None)
if (not gene):
gene = BedGene(id, record.chr, record.strand)
genesByName[id] = gene
genes.append(gene)
gene.addCDS(record.interval)
reader.close()
return genes
def readCDS(self,filename):
reader=BedReader(filename)
genes=[]
genesByName={}
while(True):
record=reader.nextRecord()
if(not record): break
if(not record.isBed6()):
raise Exception("BED file has too few fields")
id=record.name
gene=genesByName.get(id,None)
if(not gene):
gene=BedGene(id,record.chr,record.strand)
genesByName[id]=gene
genes.append(gene)
gene.addCDS(record.interval)
reader.close()
return genes
def addUTR(self, filename, genes):
hash = self.hashGenes(genes)
reader = BedReader(filename)
while (True):
record = reader.nextRecord()
if (not record): break
if (not record.isBed6()):
raise Exception("BED file has too few fields")
id = record.name
gene = hash.get(id, None)
if (not gene):
gene = BedGene(id, record.chr, record.strand)
genes.append(gene)
hash[id] = gene
gene.addUTR(record.interval)
for gene in genes:
gene.coalesce()