def init_pipeline(self):
"""initialize a new pipeline."""
## update __SAMPLES__, __SHARED__ and __GENERAL__ sections.
self.c.config_file = self.args.config_file
if self.args.input_samples:
self.c.update_sample_section(self.args.input_samples)
if self.args.setup_file:
self.c.update_shared_section(self.args.setup_file)
## make a copy of the updated config file in the working directory.
updated_cfgfile = os.path.basename(
self.args.config_file).split('.yaml')[0]
updated_cfgfile = os.path.join(self.args.working_dir,
updated_cfgfile + '_kronos.yaml')
Configurer.print2yaml(self.c.config_dict, updated_cfgfile)
## create a work flow from updated config file
wf = WorkFlow(updated_cfgfile)
samples = wf.get_samples()
if not samples:
self._make_intermediate_pipeline(self.args.pipeline_name,
updated_cfgfile, None)
else:
for sample_id, sample_dict in samples.iteritems():
new_config_file = self._make_intermediate_config_file(
sample_id, sample_dict)
pipeline_name = sample_id + '_' + self.args.pipeline_name
self._make_intermediate_pipeline(pipeline_name,
new_config_file, sample_id)
self._paste_pipelines(updated_cfgfile)
def init_pipeline(self):
"""initialize a new pipeline."""
## update __SAMPLES__, __SHARED__ and __GENERAL__ sections.
self.c.config_file = self.args.config_file
if self.args.input_samples:
self.c.update_sample_section(self.args.input_samples)
if self.args.setup_file:
self.c.update_shared_section(self.args.setup_file)
## make a copy of the updated config file in the working directory.
updated_cfgfile = os.path.basename(self.args.config_file).split('.yaml')[0]
updated_cfgfile = os.path.join(self.args.working_dir, updated_cfgfile + '_kronos.yaml')
Configurer.print2yaml(self.c.config_dict, updated_cfgfile)
## create a work flow from updated config file
wf = WorkFlow(updated_cfgfile)
samples = wf.get_samples()
if not samples:
self._make_intermediate_pipeline(self.args.pipeline_name, updated_cfgfile, None)
else:
for sample_id, sample_dict in samples.iteritems():
new_config_file = self._make_intermediate_config_file(sample_id, sample_dict)
pipeline_name = sample_id + '_' + self.args.pipeline_name
self._make_intermediate_pipeline(pipeline_name, new_config_file, sample_id)
self._paste_pipelines(updated_cfgfile)
def update_config(self): old_config_file = self.args.config_files[0] new_config_file = self.args.config_files[1] file_name = os.path.join(self.args.working_dir, self.args.output_filename + '.yaml') new_config_dict = Configurer.update_config_files(old_config_file, new_config_file) Configurer.print2yaml(new_config_dict, file_name)
def update_config(self):
old_config_file = self.args.config_files[0]
new_config_file = self.args.config_files[1]
file_name = os.path.join(self.args.working_dir,
self.args.output_filename + '.yaml')
new_config_dict = Configurer.update_config_files(
old_config_file, new_config_file)
Configurer.print2yaml(new_config_dict, file_name)
def _make_intermediate_config_file(self, sample_id, sample_dict): """make an intermediate config file from the original config_file.""" intermediate_dir = os.path.join(self.args.working_dir, 'intermediate_config_files') make_dir(intermediate_dir) temp_name = os.path.splitext(os.path.basename(self.args.config_file))[0] + '_kronos' new_file_name = os.path.join(intermediate_dir, sample_id + '_' + temp_name + '.yaml') new_config_dict = self.c.update_config_dict(sample_dict) Configurer.print2yaml(new_config_dict, new_file_name) return new_file_name
def _make_intermediate_config_file(self, sample_id, sample_dict):
"""make an intermediate config file from the original config_file."""
intermediate_dir = os.path.join(self.args.working_dir,
'intermediate_config_files')
make_dir(intermediate_dir)
temp_name = os.path.splitext(os.path.basename(
self.args.config_file))[0] + '_kronos'
new_file_name = os.path.join(intermediate_dir,
sample_id + '_' + temp_name + '.yaml')
new_config_dict = self.c.update_config_dict(sample_dict)
Configurer.print2yaml(new_config_dict, new_file_name)
return new_file_name
def make_config(self): """make a yaml config file.""" file_name = os.path.join(self.args.working_dir, self.args.output_filename + '.yaml') config_dict = Configurer.make_config_dict(self.args.components) Configurer.print2yaml(config_dict, file_name)
def make_config(self):
"""make a yaml config file."""
file_name = os.path.join(self.args.working_dir,
self.args.output_filename + '.yaml')
config_dict = Configurer.make_config_dict(self.args.components)
Configurer.print2yaml(config_dict, file_name)
