def run(self): super(JobFinalize, self).run() #shutil.copy2(self.contigs_file, self.out_files["contigs"]) shutil.copy2(self.graph_file, self.out_files["graph"]) shutil.copy2(self.polished_gfa, self.out_files["gfa"]) scaffolds = scf.generate_scaffolds(self.contigs_file, self.scaffold_links, self.out_files["assembly"]) logger.debug("---Output dir contents:----") try: ls_out = subprocess.check_output( ["ls", "-ARGg", os.path.abspath(self.args.out_dir)]) logger.debug("\n\n" + ls_out) except (subprocess.CalledProcessError, OSError): pass logger.debug("--------------------------") scf.generate_stats(self.repeat_stats, self.polished_stats, scaffolds, self.out_files["stats"]) try: os.symlink(self.out_files["assembly"], self.out_files["scaffolds"]) except OSError as e: logger.debug(e) logger.info("Final assembly: {0}".format(self.out_files["assembly"]))
def run(self): super(JobFinalize, self).run() #shutil.copy(self.contigs_file, self.out_files["contigs"]) shutil.copy(self.graph_file, self.out_files["graph"]) shutil.copy(self.polished_gfa, self.out_files["gfa"]) scaffolds = scf.generate_scaffolds(self.contigs_file, self.scaffold_links, self.out_files["assembly"]) #create the scaffolds.fasta symlink for backward compatability #try: # if os.path.lexists(self.out_files["scaffolds"]): # os.remove(self.out_files["scaffolds"]) # relative_link = os.path.relpath(self.out_files["assembly"], # self.work_dir) # os.symlink(relative_link, self.out_files["scaffolds"]) #except OSError as e: # logger.debug(e) logger.debug("---Output dir contents:----") _list_files(os.path.abspath(self.args.out_dir)) logger.debug("--------------------------") scf.generate_stats(self.repeat_stats, self.polished_stats, scaffolds, self.out_files["stats"]) logger.info("Final assembly: %s", self.out_files["assembly"])
def run(self): #shutil.copy2(self.contigs_file, self.out_files["contigs"]) shutil.copy2(self.graph_file, self.out_files["graph"]) shutil.copy2(self.polished_gfa, self.out_files["gfa"]) scaffolds = scf.generate_scaffolds(self.contigs_file, self.scaffold_links, self.out_files["scaffolds"]) scf.generate_stats(self.repeat_stats, self.polished_stats, scaffolds, self.out_files["stats"]) logger.info("Final assembly: {0}".format(self.out_files["scaffolds"]))