def run(self): logger.info("Computing rough consensus") contigs_info = aln.get_contigs_info(self.in_contigs) consensus_fasta = cons.get_consensus(self.in_alignment, self.in_contigs, contigs_info, self.args.threads, self.args.platform, self.args.min_overlap) fp.write_fasta_dict(consensus_fasta, self.out_consensus)
def run(self): logger.info("Computing rough consensus") contigs_info = aln.get_contigs_info(self.in_contigs) consensus_fasta = cons.get_consensus(self.in_alignment, contigs_info, self.args.threads) fp.write_fasta_dict(consensus_fasta, self.out_consensus) Job.run_description["stage_name"] = self.name
def run(self): logger.info("Polishing genome ({0}/{1})".format(self.stage_id, self.args.num_iters)) contigs_info = aln.get_contigs_info(self.in_contigs) logger.info("Separating alignment into bubbles") bubbles = bbl.get_bubbles(self.in_alignment, contigs_info, self.in_contigs, self.seq_platform, self.args.threads, self.args.min_overlap) logger.info("Correcting bubbles") polished_fasta = pol.polish(bubbles, self.args.threads, self.seq_platform, self.work_dir, self.stage_id) fp.write_fasta_dict(polished_fasta, self.out_consensus)