def saveFasta(self, oFileHandle, **kw): writer = FastaFile(oFileHandle, 'w') for name in self.order: writer.write(name, self.seqDict[name]) writer.close()
end = int(tokens[7]) strand = {'1': '+', '-1': '-'}[tokens[8]] try: for contig in contigData[chrom].find(start-500, end+500): annotated.add(contig.value[0]) except: pass print 'Parse toxprot alignments' iFilename = '../toxprot/tblastn_toxprot_v_genome.txt' for b in BlastFile(iFilename): chrom = b.subjectId.split(':')[0] try: for contig in contigData[chrom].find(b.sStart, b.sEnd): annotated.add(contig.value[0]) except: pass print "Write out what's left over" writer = FastaFile('unannotated_contigs.fa', 'w') for chrom in contigData: for contig in contigData[chrom].intervals: if not contig.value[0] in annotated and len(contig.value[4])>60: name,chrom,start,end,seq = contig.value writer('%s %s:%i-%i' % (name,chrom,start,end), seq) writer.close()