def get_outputs():
if not os.path.isdir('hgt_data/'):
os.makedirs('hgt_data/')
os.chdir('hgt_data/')
kh.output_hits_csv()
kh.output_groups()
# if __name__ == '__main__':
# import sys
# os.chdir('/Users/KBLaptop/computation/kvasir/data/output/dutton_genomes2/')
# mongo_init('dutton_genomes2')
# get_outputs()
def global_distance(species_1, species_2):
hits_list = all_by_all(species_1, species_2)
hits_distance = []
ssu_distance = None
for hit in hits_list:
distance = kh.get_gene_distance(str(hit[0]['dna_seq']), str(hit[1]['dna_seq']))
hits_distance.append(distance)
if hit[0]['type'] == '16S':
ssu_distance = distance
return (ssu_distance, hits_distance)