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test_lca_db_protocol.py
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test_lca_db_protocol.py
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"""
Test the behavior of LCA databases. New LCA database classes should support
all of this functionality.
"""
import pytest
import sourmash_tst_utils as utils
import sourmash
from sourmash.tax.tax_utils import MultiLineageDB
from sourmash.lca.lca_db import (LCA_Database, load_single_database)
def build_inmem_lca_db(runtmp):
# test in-memory LCA_Database
sigfile1 = utils.get_test_data('prot/protein/GCA_001593925.1_ASM159392v1_protein.faa.gz.sig')
sigfile2 = utils.get_test_data('prot/protein/GCA_001593935.1_ASM159393v1_protein.faa.gz.sig')
ss1 = sourmash.load_one_signature(sigfile1)
ss2 = sourmash.load_one_signature(sigfile2)
lineages_file = utils.get_test_data('prot/gtdb-subset-lineages.csv')
lineages = MultiLineageDB.load([lineages_file])
db = LCA_Database(ksize=19, scaled=100, moltype='protein')
ident1 = ss1.name.split(' ')[0].split('.')[0]
assert lineages[ident1]
db.insert(ss1, ident=ident1, lineage=lineages[ident1])
ident2 = ss2.name.split(' ')[0].split('.')[0]
assert lineages[ident2]
db.insert(ss2, ident=ident2, lineage=lineages[ident2])
return db
def build_json_lca_db(runtmp):
# test saved/loaded JSON database
db = build_inmem_lca_db(runtmp)
db_out = runtmp.output('protein.lca.json')
db.save(db_out, format='json')
x = load_single_database(db_out)
db_load = x[0]
return db_load
def build_sql_lca_db(runtmp):
# test saved/loaded SQL database
db = build_inmem_lca_db(runtmp)
db_out = runtmp.output('protein.lca.json')
db.save(db_out, format='sql')
x = load_single_database(db_out)
db_load = x[0]
return db_load
@pytest.fixture(params=[build_inmem_lca_db,
build_json_lca_db,
build_sql_lca_db])
def lca_db_obj(request, runtmp):
build_fn = request.param
return build_fn(runtmp)
def test_get_lineage_assignments(lca_db_obj):
# test get_lineage_assignments for a specific hash
lineages = lca_db_obj.get_lineage_assignments(178936042868009693)
assert len(lineages) == 1
lineage = lineages[0]
x = []
for tup in lineage:
if tup[0] != 'strain' or tup[1]: # ignore empty strain
x.append((tup[0], tup[1]))
assert x == [('superkingdom', 'd__Archaea'),
('phylum', 'p__Crenarchaeota'),
('class', 'c__Bathyarchaeia'),
('order', 'o__B26-1'),
('family', 'f__B26-1'),
('genus', 'g__B26-1'),
('species', 's__B26-1 sp001593925'),]
def test_hashvals(lca_db_obj):
# test getting individual hashvals
hashvals = set(lca_db_obj.hashvals)
assert 178936042868009693 in hashvals
def test_get_identifiers_for_hashval(lca_db_obj):
# test getting identifiers belonging to individual hashvals
idents = lca_db_obj.get_identifiers_for_hashval(178936042868009693)
idents = list(idents)
assert len(idents) == 1
ident = idents[0]
assert ident == 'GCA_001593925'
def test_get_identifiers_for_hashval_2(lca_db_obj):
# test systematic hashval => identifiers
all_idents = set()
for hashval in lca_db_obj.hashvals:
idents = lca_db_obj.get_identifiers_for_hashval(hashval)
#idents = list(idents)
all_idents.update(idents)
all_idents = list(all_idents)
print(all_idents)
assert len(all_idents) == 2
assert 'GCA_001593925' in all_idents
assert 'GCA_001593935' in all_idents
def test_downsample_scaled(lca_db_obj):
# check the downsample_scaled method
assert lca_db_obj.scaled == 100
lca_db_obj.downsample_scaled(500)
assert lca_db_obj.scaled == 500
def test_downsample_scaled_fail(lca_db_obj):
# check the downsample_scaled method - should fail if lower scaled.
assert lca_db_obj.scaled == 100
with pytest.raises(ValueError):
lca_db_obj.downsample_scaled(50)