def cluster_contigs(self): default_clustering = constants.blank_default if self.blank else constants.single_default for config_name in self.clustering_configs: config_path = self.clustering_configs[config_name] config = ClusteringConfiguration( config_path, self.output_directory, db_paths=self.database_paths, row_ids_of_interest=self.split_names) try: clustering_id, newick = clustering.order_contigs_simple( config, distance=self.distance, linkage=self.linkage, progress=self.progress) except Exception as e: self.run.warning('Clustering has failed for "%s": "%s"' % (config_name, e)) self.progress.end() continue dbops.add_hierarchical_clustering_to_db(self.profile_db_path, config_name, newick, distance=self.distance, linkage=self.linkage, \ make_default=config_name == default_clustering, run=self.run)
def cluster_contigs_anvio(self): # clustering of contigs is done for each configuration file under static/clusterconfigs/merged directory; # at this point we don't care what those recipes really require because we already merged and generated # every data file that may be required. if not self.skip_hierarchical_clustering: for config_name in self.clustering_configs: config_path = self.clustering_configs[config_name] config = ClusteringConfiguration( config_path, self.output_directory, db_paths=self.database_paths, row_ids_of_interest=self.split_names) try: newick = clustering.order_contigs_simple( config, progress=self.progress) except Exception as e: self.run.warning('Clustering has failed for "%s": "%s"' % (config_name, e)) self.progress.end() continue dbops.add_hierarchical_clustering_to_db( self.profile_db_path, config_name, newick, make_default=config_name == constants.merged_default, run=self.run)
def cluster_contigs(self): for config_name in self.clustering_configs: config_path = self.clustering_configs[config_name] config = ClusteringConfiguration(config_path, self.output_directory, db_paths = self.database_paths, row_ids_of_interest = self.split_names) try: newick = clustering.order_contigs_simple(config, progress = self.progress) except Exception as e: self.run.warning('Clustering has failed for "%s": "%s"' % (config_name, e)) self.progress.end() continue dbops.add_hierarchical_clustering_to_db(self.profile_db_path, config_name, newick, make_default = config_name == constants.single_default, run = self.run)
def cluster_contigs_anvio(self): # clustering of contigs is done for each configuration file under static/clusterconfigs/merged directory; # at this point we don't care what those recipes really require because we already merged and generated # every metadata file that may be required. if not self.skip_hierarchical_clustering: for config_name in self.clustering_configs: config_path = self.clustering_configs[config_name] config = ClusteringConfiguration(config_path, self.output_directory, db_paths = self.database_paths, row_ids_of_interest = self.split_names) try: newick = clustering.order_contigs_simple(config, progress = self.progress) except Exception as e: self.run.warning('Clustering has failed for "%s": "%s"' % (config_name, e)) self.progress.end() continue dbops.add_hierarchical_clustering_to_db(self.profile_db_path, config_name, newick, make_default = config_name == constants.merged_default, run = self.run)