def test_fastani_small_num_pairs(tmpdir):
"""Test FastANI cache on small number of pairs."""
db_file = tmpdir.mkdir("sub").join("tmp.db").strpath
qid = 'GCF_000009045.1'
rid = 'GCF_000186085.1'
q_gf = './tests/data/GCF_000009045.1.fna.gz'
r_gf = './tests/data/GCF_000186085.1.fna.gz'
gid_pairs = [(qid, rid), (rid, qid)]
genome_files = {qid: q_gf,
rid: r_gf}
fastani = FastANI(db_file, 1)
ani_af = fastani.pairs(gid_pairs, genome_files, report_progress=True, initial_cache_check=True)
# exact values will depend on FastANI version, but should be reater than these bound
assert ani_af[qid][rid][0] > 99.5
assert ani_af[qid][rid][1] > 0.995
assert ani_af[rid][qid][0] > 99.5
assert ani_af[rid][qid][1] > 0.995
# re-test results now that results have been cached
ani_af = fastani.pairs(gid_pairs, genome_files, report_progress=True, initial_cache_check=True)
assert ani_af[qid][rid][0] > 99.5
assert ani_af[qid][rid][1] > 0.995
assert ani_af[rid][qid][0] > 99.5
assert ani_af[rid][qid][1] > 0.995
def test_fastani_large_num_pairs(tmpdir):
"""Test FastANI cache on large number of pairs."""
db_file = tmpdir.mkdir("sub").join("tmp.db").strpath
qid = 'GCF_000009045.1'
rid = 'GCF_000186085.1'
q_gf = './tests/data/GCF_000009045.1.fna.gz'
r_gf = './tests/data/GCF_000186085.1.fna.gz'
# artificial duplicate pairs to force using multiprocessing
gid_pairs = [(qid, rid), (rid, qid),
(qid, rid), (rid, qid),
(qid, rid), (rid, qid),
(qid, rid), (rid, qid)]
genome_files = {qid: q_gf,
rid: r_gf}
fastani = FastANI(db_file, 1)
fastani.DB_BATCH_SIZE = 1 # force saving to cache to ensure code is tested
ani_af = fastani.pairs(gid_pairs, genome_files, report_progress=True, initial_cache_check=True)
# exact values will depend on FastANI version, but should be reater than these bound
assert ani_af[qid][rid][0] > 99.5
assert ani_af[qid][rid][1] > 0.995
assert ani_af[rid][qid][0] > 99.5
assert ani_af[rid][qid][1] > 0.995
# re-test results now that results have been cached
ani_af = fastani.pairs(gid_pairs, genome_files, report_progress=True, initial_cache_check=True)
assert ani_af[qid][rid][0] > 99.5
assert ani_af[qid][rid][1] > 0.995
assert ani_af[rid][qid][0] > 99.5
assert ani_af[rid][qid][1] > 0.995
def test_object_db_creation(tmpdir):
"""Test creation of FastANI object with SQlite database."""
db_file = tmpdir.mkdir("sub").join("tmp.db").strpath
fastani = FastANI(db_file, 1)
assert fastani.num_db_rows() is None
def test_fastani_invalid_input(tmpdir):
"""Test FastANI on invalid input."""
db_file = tmpdir.mkdir("sub").join("tmp.db").strpath
qid = 'invalid1'
rid = 'invalid2'
q_gf = 'does_not_exist.fna'
r_gf = 'does_not_exist.fna'
fastani = FastANI(db_file, 1)
with pytest.raises(FastANIError):
fastani.fastani(qid, rid, q_gf, r_gf)
def test_mean_ani():
"""Test mean methods for combining reciprocal pairs."""
ani_af = {}
ani_af['g1'] = {}
ani_af['g1']['g2'] = (90, 0.95)
ani_af['g2'] = {}
ani_af['g2']['g1'] = (95, 0.90)
fastani = FastANI(None, 1)
ani, af = fastani.mean_ani(ani_af, 'g1', 'g2')
assert ani == 92.5
assert af == 0.925
def test_symmetric_ani():
"""Test symmetrical (max) methods for combining reciprocal pairs."""
ani_af = {}
ani_af['g1'] = {}
ani_af['g1']['g2'] = (90, 0.95)
ani_af['g2'] = {}
ani_af['g2']['g1'] = (95, 0.90)
fastani = FastANI(None, 1)
ani, af = fastani.symmetric_ani(ani_af, 'g1', 'g2')
assert ani == 95
assert af == 0.95
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'
def test_fastani_valid_input(tmpdir):
"""Test FastANI on valid input."""
db_file = tmpdir.mkdir("sub").join("tmp.db").strpath
qid = 'GCF_000009045.1'
rid = 'GCF_000186085.1'
q_gf = './tests/data/GCF_000009045.1.fna.gz'
r_gf = './tests/data/GCF_000186085.1.fna.gz'
fastani = FastANI(db_file, 1)
ani_af = fastani.fastani(qid, rid, q_gf, r_gf)
assert ani_af[0] == 'GCF_000009045.1'
assert ani_af[1] == 'GCF_000186085.1'
# exact values will depend on FastANI version, but should be reater than these bound
assert ani_af[2] > 99.5
assert ani_af[3] > 0.995
def test_write_matrices(tmpdir):
"""Test ANI and AF matrices."""
out_file = tmpdir.mkdir("output").join("results.tsv").strpath
ani_af = {}
ani_af['g1'] = {}
ani_af['g1']['g1'] = (100, 1.0)
ani_af['g1']['g2'] = (90, 0.95)
ani_af['g2'] = {}
ani_af['g2']['g2'] = (100, 1.0)
ani_af['g2']['g1'] = (95, 0.90)
fastani = FastANI(None, 1)
fastani.write_ani_matrix(out_file, ani_af)
# test ANI matrix
fin = open(out_file)
assert fin.readline().rstrip() == '\tg1\tg2'
assert fin.readline().rstrip() == 'g1\t100\t90'
assert fin.readline().rstrip() == 'g2\t95\t100'
fin.close()
# test AF matrix
fastani.write_af_matrix(out_file, ani_af)
fin = open(out_file)
assert fin.readline().rstrip() == '\tg1\tg2'
assert fin.readline().rstrip() == 'g1\t1.0\t0.95'
assert fin.readline().rstrip() == 'g2\t0.9\t1.0'
fin.close()
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.')