def fastani(self, args):
"""Run FastANI and cache results."""
query_files = self._input_files(args.query_genomes, args.file_ext,
args.validate_genome_files)
ref_files = self._input_files(args.ref_genomes, args.file_ext,
args.validate_genome_files)
make_sure_path_exists(args.output_dir)
self.logger.info(
'Identified {:,} query and {:,} reference genomes.'.format(
len(query_files), len(ref_files)))
# get genome pairs to be considered
gid_pairs, genome_files = self._genome_comparisons(
query_files, ref_files, args.ref_to_query)
self.logger.info('Calculating ANI between {:,} genome pairs.'.format(
len(gid_pairs)))
# calculate ANI between genome pairs
start = time.time()
fastani = FastANI(args.ani_db_file, args.cpus)
try:
ani_af = fastani.pairs(
gid_pairs,
genome_files,
report_progress=True,
initial_cache_check=args.initial_cache_check)
results_file = os.path.join(args.output_dir, 'ani_af.tsv')
except Exception as e:
print(e)
raise
finally:
fastani.write_cache()
fastani.write_ani_af(results_file, ani_af)
if args.query_genomes == args.ref_genomes:
# since pairwise calculations were performed
# also write out results as matrices
ani_matrix_file = os.path.join(args.output_dir, 'ani_matrix.tsv')
fastani.write_ani_matrix(ani_matrix_file, ani_af)
af_matrix_file = os.path.join(args.output_dir, 'af_matrix.tsv')
fastani.write_ani_matrix(af_matrix_file, ani_af)
elapsed_time_str = str(
datetime.timedelta(seconds=round(time.time() - start)))
self.logger.info(
f'Time to calculate ANI values (h:mm:ss): {elapsed_time_str}')
self.logger.info('Done.')
def test_write_ani_af(tmpdir):
"""Test writing of results."""
out_file = tmpdir.mkdir("output").join("results.tsv").strpath
ani_af = {}
ani_af['g1'] = {}
ani_af['g1']['g2'] = (90, 0.95)
fastani = FastANI(None, 1)
fastani.write_ani_af(out_file, ani_af)
fin = open(out_file)
assert fin.readline().strip() == 'Query\tReference\tANI\tAF'
assert fin.readline().strip() == 'g1\tg2\t90\t0.95'