def setUp(self):
datadir = get_data_dir()
self.infile = datadir + "test.fasta"
self.outfile = datadir + "test_temp.txt"
# args = parser.parse_args(["-h"])
self.BLAST = runBLAST(self.infile, self.outfile)
# file_name = "/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/test.fasta"
# file_name = "/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/test_blastx.fasta"
outfile = "/home/sw167/Postdoc/Project_Fungi/data/test_out.txt"
# args = parser.parse_args(["-h"])
file_name = "/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/Euro_Blast_All.fas"
outfile = "/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/Euro_Blast_All_130202.out"
args = parser.parse_args([file_name, outfile])
# args = parser.parse_args()
# main(args)
BLAST = runBLAST(args.file_name, args.outfile)
# BLAST.run()
# BLAST.custom_Update()
# BLAST.check2()
taxa_list_file = "/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/Euro_Blast_All_130202.out.Taxa_67Genes"
outfile = "/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/Euro_Blast_All_130202.out.Seqs_67genes"
taxa_file = open(taxa_list_file, "r")
efetch_taxa_list = pickle.load(taxa_file)
exist_ref_seq_list = open("/home/sw167/Postdoc/Project_Fungi/autoBLAST/data/Eurotio_alltaxa.list", "r")
# infile = open(file_name, "r")
efetch_taxa_set = set()
for taxa in efetch_taxa_list:
taxa = taxa.lower()
efetch_taxa_set.add(taxa)