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"]))