def initialize_project(self):
'''Wrapper for building the project.
1. Load the settings
2. Load the assembly
3. Load the samples
4. Set the directory structure
'''
self.logger.info('Project Name: {0.name}'.format(self))
# Settings
self.settings = PipelineSettings(self.args, self.PATH)
self.logger.info('Baseline Threads: {0.threads}'.format(self.settings))
self.logger.info('Clip Adapters: {0.clipping}'.format(self.settings))
if self.settings.clipping:
self.logger.info('Minimum read length: {0.min_length}'.format(
self.settings))
self.logger.info('Minimum MAPQ: {0.min_map_q}'.format(self.settings))
self.logger.info('Aligners: {0}'.format(self.settings.aln_list))
self.logger.info('Somatic Mutation Detectors: {0}'.format(
self.settings.smd_list))
# Assembly info
self._set_assembly()
self.logger.info('Reference Name: {0}'.format(
self.assembly['refname']))
# Samples
self.samples.load_samples(os.path.abspath(self.args.metadata),
self.PATH, self.name)
# File structure
self._set_project_files()
