def test_lca_index_signatures_method():
# test 'signatures' method from base class Index
filename = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(filename)
siglist = list(db.signatures())
assert len(siglist) == 2
def test_load_single_db():
filename = utils.get_test_data('lca/delmont-1.lca.json')
db, ksize, scaled = lca_utils.load_single_database(filename)
print(db)
assert ksize == 31
assert scaled == 10000
def test_search_db_scaled_lt_sig_scaled():
dbfile = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(dbfile)
sig = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'))
sig.minhash = sig.minhash.downsample_scaled(100000)
with pytest.raises(ValueError) as e:
results = db.search(sig, threshold=.01, ignore_abundance=True)
def test_lca_index_find_method():
# test 'signatures' method from base class Index
filename = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(filename)
sig = next(iter(db.signatures()))
with pytest.raises(NotImplementedError) as e:
db.find(None)
def test_gather_db_scaled_gt_sig_scaled():
dbfile = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(dbfile)
sig = sourmash.load_one_signature(utils.get_test_data('47.fa.sig'))
results = db.gather(sig, threshold=.01, ignore_abundance=True)
match_sig = results[0][1]
sig.minhash = sig.minhash.downsample_scaled(10000)
assert sig.minhash == match_sig.minhash
def test_db_idx_to_ident():
dbfile = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(dbfile)
d = db.idx_to_ident
items = list(d.items())
items.sort()
assert len(items) == 2
print(items)
assert items == [(32, 'NC_009665'), (48, 'NC_011663')]
def test_db_lid_to_idx():
dbfile = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(dbfile)
d = db.lid_to_idx
items = list(d.items())
items.sort()
assert len(items) == 2
print(items)
assert items == [(32, {32}), (48, {48})]
def main():
p = argparse.ArgumentParser()
p.add_argument('lca_db')
p.add_argument('genome', nargs='+')
p.add_argument('output')
p.add_argument('--fragment', default=100000, type=int)
args = p.parse_args()
db, ksize, scaled = lca_utils.load_single_database(args.lca_db)
mh_factory = sourmash.MinHash(n=0, ksize=ksize, scaled=scaled)
print('**', ksize, scaled)
n = 0
m = 0
sum_bp = 0
sum_missed_bp = 0
outfp = open(args.output, 'wt')
w = csv.writer(outfp)
w.writerow(['filename', 'contig', 'begin', 'end', 'lca', 'lca_rank'])
#
# iterate over all contigs in genome file
#
for genome in args.genome:
for record in screed.open(genome):
# fragment longer contigs into smaller regions?
for start in range(0, len(record.sequence), args.fragment):
seq = record.sequence[start:start + args.fragment]
n += 1
sum_bp += len(seq)
mh = mh_factory.copy_and_clear()
mh.add_sequence(seq, force=True)
if not mh:
sum_missed_bp += len(seq)
continue
lineage_counts = summarize(mh.get_mins(), [db], 1)
for k in lineage_counts:
lca = lca_utils.display_lineage(k, truncate_empty=False)
try:
lca_rank = k[-1].rank
except IndexError:
lca_rank = "none"
w.writerow((genome, record.name, start,
start + args.fragment, lca, lca_rank))
m += 1
min_value = min(mh.get_mins())
return 0
def test_db_lineage_to_lids():
dbfile = utils.get_test_data('lca/47+63.lca.json')
db, ksize, scaled = lca_utils.load_single_database(dbfile)
d = db.lineage_to_lids
items = list(d.items())
items.sort()
assert len(items) == 2
print(items)
lin1 = items[0][0][-1]
assert lin1.rank == 'strain'
assert lin1.name == 'Shewanella baltica OS185'
lin1 = items[1][0][-1]
assert lin1.rank == 'strain'
assert lin1.name == 'Shewanella baltica OS223'
def test_db_repr():
filename = utils.get_test_data('lca/delmont-1.lca.json')
db, ksize, scaled = lca_utils.load_single_database(filename)
assert repr(db) == "LCA_Database('{}')".format(filename)
