other_gbk_folder =os.path.abspath('data/input/other/')
exp_name = datetime.datetime.now().strftime('%Y%m%d%H%M')
mongo_init(exp_name)
reset_database(exp_name)
new_folder = 'data/output/{0}/'.format(exp_name)
if not os.path.isdir(new_folder):
os.makedirs(new_folder)
os.chdir(new_folder)
print 'Checking and importing core genomes...'
for the_file in os.listdir(core_gbk_folder):
path_to_file = '{0}/{1}'.format(core_gbk_folder, the_file)
DataImport.import_file(path_to_file, 'core')
print 'Checking and importing other genomes...'
for the_file in os.listdir(other_gbk_folder):
path_to_file = '{0}/{1}'.format(other_gbk_folder, the_file)
DataImport.import_file(path_to_file, 'other')
KvasirBlast.make_blast_db('core')
KvasirBlast.make_blast_db('other')
KvasirBlast.core_hgt_blast(perc_identity='90')
# KvasirBlast.core_hgt_blast(perc_identity='95')
# KvasirBlast.core_hgt_blast(perc_identity='99')
KvasirBlast.blast_to_db(perc_identity='90')
# KvasirBlast.blast_to_db(perc_identity='95')
