def run(self):
super(JobPolishing, self).run()
if not os.path.isdir(self.polishing_dir):
os.mkdir(self.polishing_dir)
pol.polish(self.in_contigs, self.args.reads, self.polishing_dir,
self.args.num_iters, self.args.threads, self.args.platform,
output_progress=True)
polished_file = os.path.join(self.polishing_dir, "polished_{0}.fasta"
.format(self.args.num_iters))
pol.generate_polished_edges(self.in_graph_edges, self.in_graph_gfa,
polished_file,
self.polishing_dir, self.args.platform,
self.args.threads)
def run(self):
super(JobPolishing, self).run()
if not os.path.isdir(self.polishing_dir):
os.mkdir(self.polishing_dir)
contigs, stats = \
pol.polish(self.in_contigs, self.args.reads, self.polishing_dir,
self.args.num_iters, self.args.threads, self.args.platform,
output_progress=True)
#contigs = os.path.join(self.polishing_dir, "polished_1.fasta")
#stats = os.path.join(self.polishing_dir, "contigs_stats.txt")
pol.filter_by_coverage(self.args, stats, contigs,
self.out_files["stats"], self.out_files["contigs"])
pol.generate_polished_edges(self.in_graph_edges, self.in_graph_gfa,
self.out_files["contigs"],
self.polishing_dir, self.args.platform,
self.args.threads)
os.remove(contigs)
def run(self):
super(JobPolishing, self).run()
if not os.path.isdir(self.polishing_dir):
os.mkdir(self.polishing_dir)
contigs, stats = \
pol.polish(self.in_contigs, self.args.reads, self.polishing_dir,
self.args.num_iters, self.args.threads, self.args.platform,
self.args.read_type, output_progress=True)
#contigs = os.path.join(self.polishing_dir, "polished_1.fasta")
#stats = os.path.join(self.polishing_dir, "contigs_stats.txt")
pol.filter_by_coverage(self.args, stats, contigs,
self.out_files["stats"],
self.out_files["contigs"])
pol.generate_polished_edges(self.in_graph_edges, self.in_graph_gfa,
self.out_files["contigs"],
self.polishing_dir, self.args.platform,
stats, self.args.threads)
os.remove(contigs)
if os.path.getsize(self.out_files["contigs"]) == 0:
raise asm.AssembleException("No contigs were assembled - "
"pipeline stopped")