34d621b7f00c1cd42f34eeae1443c24563786fc3,anvio/tables/hmmhits.py,TablesForHMMHits,populate_search_tables,#TablesForHMMHits#Any#,69

Before Change

                                                           target_files_dict["%s:CONTIG" % alphabet],
                                                           rna_alphabet=True if alphabet=="RNA" else False)

        commander = HMMer(target_files_dict, num_threads_to_use=self.num_threads_to_use)

        for source in sources:
            alphabet, context = utils.anvio_hmm_target_term_to_alphabet_and_context(sources[source]["target"])

            kind_of_search = sources[source]["kind"]
            domain = sources[source]["domain"]
            all_genes_searched_against = sources[source]["genes"]
            hmm_model = sources[source]["model"]
            reference = sources[source]["ref"]
            noise_cutoff_terms = sources[source]["noise_cutoff_terms"]

            hmm_scan_hits_txt = commander.run_hmmscan(source,
                                                      alphabet,
                                                      context,
                                                      kind_of_search,
                                                      domain,
                                                      len(all_genes_searched_against),
                                                      hmm_model,
                                                      reference,
                                                      noise_cutoff_terms)

            if not hmm_scan_hits_txt:
                search_results_dict = {}
            else:
                parser = parser_modules["search"]["hmmscan"](hmm_scan_hits_txt, alphabet=alphabet, context=context)
                search_results_dict = parser.get_search_results()

            if not len(search_results_dict):
                run.info_single("The HMM source "%s" returned 0 hits. SAD (but it"s stil OK)." % source, nl_before=1)


            if context == "CONTIG":
                // we are in trouble here. because our search results dictionary contains no gene calls, but contig
                // names that contain our hits. on the other hand, the rest of the code outside of this if statement
                // expects a `search_results_dict` with gene callers id in it. so there are two things we need to do

After Change

        for source in sources:
            threads = []
            for i in range(self.num_threads_to_use):
                new_thread = Thread(target=hmm_worker, args=(i, source))
                new_thread.start()
                threads.append(new_thread)

            for t in threads:
                t.join()

Instances