def generate_config(self, cfg):
if sys.version.startswith("2."):
import pyyaml2 as pyyaml
elif sys.version.startswith("3."):
import pyyaml3 as pyyaml
self.cfg = merge_configs(cfg["error_correction"], cfg["common"])
self.output_files["corrected_dataset_yaml_filename"] = os.path.join(
self.cfg.output_dir, "corrected.yaml")
self.cfg.__dict__["dataset_yaml_filename"] = cfg[
"dataset"].yaml_filename
addsitedir(self.ext_python_modules_home)
if not os.path.isdir(self.cfg.output_dir):
os.makedirs(self.cfg.output_dir)
# not all reads need processing
if support.get_lib_ids_by_type(self.dataset_data,
options_storage.LONG_READS_TYPES):
not_used_dataset_data = support.get_libs_by_type(
self.dataset_data, options_storage.LONG_READS_TYPES)
to_correct_dataset_data = support.rm_libs_by_type(
self.dataset_data, options_storage.LONG_READS_TYPES)
to_correct_dataset_yaml_filename = os.path.join(
self.cfg.output_dir, "to_correct.yaml")
self.cfg.not_used_dataset_yaml_filename = os.path.join(
self.cfg.output_dir, "dont_correct.yaml")
with open(to_correct_dataset_yaml_filename, 'w') as f:
pyyaml.dump(to_correct_dataset_data,
f,
default_flow_style=False,
default_style='"',
width=float("inf"))
with open(self.cfg.not_used_dataset_yaml_filename, 'w') as f:
pyyaml.dump(not_used_dataset_data,
f,
default_flow_style=False,
default_style='"',
width=float("inf"))
self.cfg.dataset_yaml_filename = to_correct_dataset_yaml_filename
else:
self.cfg.not_used_dataset_yaml_filename = ""
for stage in self.stages:
stage.generate_config(self.cfg)
def generate_config(self, cfg):
if not os.path.isdir(self.dir_for_split_reads):
os.makedirs(self.dir_for_split_reads)
if not os.path.isdir(self.tmp_dir):
os.makedirs(self.tmp_dir)
for stage in self.stages:
stage.generate_config(cfg)
if sys.version.startswith("2."):
import pyyaml2 as pyyaml
elif sys.version.startswith("3."):
import pyyaml3 as pyyaml
with open(options_storage.args.dataset_yaml_filename, 'w') as f:
pyyaml.dump(self.dataset_data,
f,
default_flow_style=False,
default_style='"',
width=float("inf"))
def generate_config(self, cfg):
for stage in self.stages:
stage.generate_config(self.cfg)