def parseFasta(self, fasta_f, fasta_type): print BtLog.status_d["1"] % ("FASTA", fasta_f) self.assembly_f = abspath(fasta_f) if fasta_type: # Set up CovLibObj for coverage in assembly header self.covLibs[fasta_type] = CovLibObj(fasta_type, fasta_type, fasta_f) for name, seq in BtIO.readFasta(fasta_f): blObj = BlObj(name, seq) if not blObj.name in self.dict_of_blobs: self.seqs += 1 self.length += blObj.length self.n_count += blObj.n_count if fasta_type: cov = BtIO.parseCovFromHeader(fasta_type, blObj.name) self.covLibs[fasta_type].cov_sum += cov blObj.addCov(fasta_type, cov) self.order_of_blobs.append(blObj.name) self.dict_of_blobs[blObj.name] = blObj else: BtLog.error("5", blObj.name) if self.seqs == 0 or self.length == 0: BtLog.error("1")
def parseFasta(self, fasta_f, fasta_type): print BtLog.status_d['1'] % ('FASTA', fasta_f) self.assembly_f = abspath(fasta_f) if (fasta_type): # Set up CovLibObj for coverage in assembly header self.covLibs[fasta_type] = CovLibObj(fasta_type, fasta_type, fasta_f) for name, seq in BtIO.readFasta(fasta_f): blObj = BlObj(name, seq) if not blObj.name in self.dict_of_blobs: self.seqs += 1 self.length += blObj.length self.n_count += blObj.n_count if (fasta_type): cov = BtIO.parseCovFromHeader(fasta_type, blObj.name) self.covLibs[fasta_type].cov_sum += cov blObj.addCov(fasta_type, cov) self.order_of_blobs.append(blObj.name) self.dict_of_blobs[blObj.name] = blObj else: BtLog.error('5', blObj.name) if self.seqs == 0 or self.length == 0: BtLog.error('1')