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):
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")
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")
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")
