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unpublished = True
if filteredScrape.unpublished is True: # use unpublished data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unpublished = True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if filteredScrape.data.otu_dict[key]['^ncbi:title'] == "unpublished":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
