def test_add_local(): data_obj = pickle.load(open("tests/data/precooked/tiny_dataobj.p", 'rb')) data_obj.workdir = absworkdir ids = IdDicts(conf, workdir=data_obj.workdir) ids.acc_ncbi_dict = pickle.load(open("tests/data/precooked/tiny_acc_map.p", "rb")) if not os.path.exists("{}".format(workdir)): os.makedirs("{}".format(workdir)) if os.path.exists(otu_jsonfi_local): otu_json_local = json.load(open(otu_jsonfi_local)) else: otu_json_local = OtuJsonDict(id_to_spn_addseq, ids) json.dump(otu_json_local, open(otu_jsonfi_local, "w")) # Now combine the data, the ids, and the configuration into a single physcraper scrape object filteredScrape = PhyscraperScrape(data_obj, ids) filteredScrape.blacklist = blacklist if add_local_seq is not None: filteredScrape.unpublished = True if filteredScrape.unpublished is True: # use unpublished data # filteredScrape.unpublished = True filteredScrape.data.unpubl_otu_json = otu_json_local filteredScrape.write_unpubl_blastdb(add_local_seq) # filteredScrape.make_otu_dict_entry_unpubl() filteredScrape.run_blast_wrapper() filteredScrape.read_blast_wrapper() filteredScrape.remove_identical_seqs() test = False for key in filteredScrape.data.otu_dict.keys(): if '^ncbi:title' in filteredScrape.data.otu_dict[key].keys(): if filteredScrape.data.otu_dict[key]['^ncbi:title'] == "unpublished": test = True break assert test == True