def run(self):
super(JobAssembly, self).run()
if not os.path.isdir(self.assembly_dir):
os.mkdir(self.assembly_dir)
asm.assemble(self.args, Job.run_params, self.assembly_filename,
self.log_file, self.args.asm_config, )
if os.path.getsize(self.assembly_filename) == 0:
raise asm.AssembleException("No disjointigs were assembled - "
"please check if the read type and genome "
"size parameters are correct")
asm_len, asm_n50 = scf.short_statistics(self.assembly_filename)
logger.debug("Disjointigs length: {0}, N50: {1}".format(asm_len, asm_n50))
def run(self):
if not os.path.isdir(self.assembly_dir):
os.mkdir(self.assembly_dir)
asm.assemble(
self.args,
Job.run_params,
self.assembly_filename,
self.log_file,
self.args.asm_config,
)
if os.path.getsize(self.assembly_filename) == 0:
raise asm.AssembleException(
"No contigs were assembled - "
"please check if the read type and genome "
"size parameters are correct")