def _log_current_status(contigs,cluster_prob,p,z,run): clustering = _get_current_clustering(contigs,p,z) Output.write_clustering_result(clustering,cluster_prob ,p,arguments=None,tmpfile=True,tmpfile_suffix=run)
contigs,idxcon = _get_contigs(args.composition_file,args.kmer) coverage,idxcov = _get_coverage(args.coverage_file,args.first_data,args.last_data) contigs = np.hstack(contigs,coverage) params["first_data"] = args.first_data params["last_data"] = args.last_data params["read_length"] = args.read_length outfile = "_".join([args.composition_file,args.coverage_file]) except ImportError: print "Failed to load module {0}.{1}. Will now exit".format(args.model_type,args.model) sys.exit(-1) #============================= #Prep output settings #============================= #TODO: Needs to be fixed to allow only coverage etc. Output.set_output_path(outfile,args) #============================= #Calling clustering #============================= (clusters,clust_prob,centroids) = main(cluster_func, contigs, p, args.cluster_count,args.epsilon,args.iterations, \ args.runs,args.verbose,args.serial, **params) #============================= #Printing Results #============================= Output.write_clustering_result(clusters,clust_prob,centroids,idx,args) #============================= #Preprocess timeseries data for coverage
contigs,idxcon = _get_contigs(args.composition_file,args.kmer) coverage,idxcov = _get_coverage(args.coverage_file,args.first_data,args.last_data) contigs = np.hstack(contigs,coverage) params["first_data"] = args.first_data params["last_data"] = args.last_data params["read_length"] = args.read_length outfile = "_".join([args.composition_file,args.coverage_file]) except ImportError: print "Failed to load module {0}.{1}. Will now exit".format(args.model_type,args.model) sys.exit(-1) #============================= #Prep output settings #============================= #TODO: Needs to be fixed to allow only coverage etc. Output.set_output_path(outfile,args) #============================= #Calling clustering #============================= (clusters,clust_prob,responsibilities, probability_parameters) = main(cluster_func, contigs, p, args.cluster_count,args.epsilon,args.iterations, \ args.runs,args.verbose,args.serial, **params) #============================= #Printing Results #============================= Output.write_clustering_result(clusters,clust_prob,responsibilities, probability_parameters,idx,args) #============================= #Preprocess timeseries data for coverage