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 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
#!/usr/bin/env python #========================================================================= # This is OPEN SOURCE SOFTWARE governed by the Gnu General Public # License (GPL) version 3, as described at www.opensource.org. # Copyright (C)2016 William H. Majoros ([email protected]). #========================================================================= from __future__ import (absolute_import, division, print_function, unicode_literals, generators, nested_scopes, with_statement) from builtins import (bytes, dict, int, list, object, range, str, ascii, chr, hex, input, next, oct, open, pow, round, super, filter, map, zip) from BedReader import BedReader BASE = "/Users/bmajoros/python/test/data" filename = BASE + "/DEGs_downreg.FDR_0.1.TSS.protein_coding.bed" reader = BedReader(filename) while (True): rec = reader.nextRecord() if (rec is None): break begin = rec.getBegin() end = rec.getEnd() print(begin, "-", end, sep="", end="") print("\t" + rec.name + "\t" + str(rec.score) + "\t" + rec.strand) reader.close()
#!/usr/bin/env python #========================================================================= # This is OPEN SOURCE SOFTWARE governed by the Gnu General Public # License (GPL) version 3, as described at www.opensource.org. # Copyright (C)2016 William H. Majoros ([email protected]). #========================================================================= from __future__ import (absolute_import, division, print_function, unicode_literals, generators, nested_scopes, with_statement) from builtins import (bytes, dict, int, list, object, range, str, ascii, chr, hex, input, next, oct, open, pow, round, super, filter, map, zip) from BedReader import BedReader BASE="/Users/bmajoros/python/test/data" filename=BASE+"/DEGs_downreg.FDR_0.1.TSS.protein_coding.bed" reader=BedReader(filename) while(True): rec=reader.nextRecord() if(rec is None): break begin=rec.getBegin() end=rec.getEnd() print(begin,"-",end,sep="",end="") print("\t"+rec.name+"\t"+str(rec.score)+"\t"+rec.strand) reader.close()
