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()