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)