def run(self):
super(JobContigger, self).run()
if not os.path.isdir(self.work_dir):
os.mkdir(self.work_dir)
logger.info("Generating contigs")
repeat.generate_contigs(self.args, Job.run_params, self.repeat_graph_edges,
self.work_dir, self.log_file, self.args.asm_config,
self.repeat_graph, self.reads_alignment)
def run(self):
super(JobContigger, self).run()
if not os.path.isdir(self.work_dir):
os.mkdir(self.work_dir)
logger.info("Generating contigs")
repeat.generate_contigs(self.args, Job.run_params,
self.repeat_graph_edges, self.work_dir,
self.log_file, self.args.asm_config,
self.repeat_graph, self.reads_alignment)
if os.path.getsize(self.out_files["contigs"]) == 0:
raise asm.AssembleException("No contigs were assembled - "
"pipeline stopped")