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")