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from tempfile import NamedTemporaryFile
import pytest
from sourmash.nodegraph import (
Nodegraph,
extract_nodegraph_info,
calc_expected_collisions,
)
import sourmash_tst_utils as utils
def test_nodegraph_to_khmer_basic():
pytest.importorskip("khmer")
ng_file = utils.get_test_data(".sbt.v3/internal.0")
sourmash_ng = Nodegraph.load(ng_file)
khmer_sm_ng = sourmash_ng.to_khmer_nodegraph()
assert sourmash_ng.ksize() == khmer_sm_ng.ksize()
def test_nodegraph_khmer_compare():
khmer = pytest.importorskip("khmer")
khmer_ng = khmer.Nodegraph(3, 23, 6)
khmer_ng.count("ACG")
khmer_ng.count("TTA")
khmer_ng.count("CGA")
sm_ng = Nodegraph(3, 23, 6)
sm_ng.count("ACG")
sm_ng.count("TTA")
sm_ng.count("CGA")
assert sm_ng.ksize() == khmer_ng.ksize()
assert sm_ng.hashsizes() == khmer_ng.hashsizes()
assert sm_ng.get("ACG")
assert sm_ng.get("TTA")
assert sm_ng.get("CGA")
assert khmer_ng.get("ACG")
assert khmer_ng.get("TTA")
assert khmer_ng.get("CGA")
def test_nodegraph_same_file():
khmer = pytest.importorskip("khmer")
try:
load_nodegraph = khmer.load_nodegraph
except AttributeError:
load_nodegraph = khmer.Nodegraph.load
ng_file = utils.get_test_data(".sbt.v3/internal.0")
with open(ng_file, "rb") as f:
ng_data = f.read()
sourmash_ng = Nodegraph.load(ng_file)
khmer_sm_ng = sourmash_ng.to_khmer_nodegraph()
khmer_ng = load_nodegraph(ng_file)
with (
NamedTemporaryFile() as f1,
NamedTemporaryFile() as f2,
NamedTemporaryFile() as f3,
):
sourmash_ng.save(f1.name)
khmer_sm_ng.save(f2.name)
khmer_ng.save(f3.name)
f1.seek(0)
sm_data = f1.read()
f2.seek(0)
kh_sm_data = f2.read()
f3.seek(0)
kh_data = f3.read()
assert extract_nodegraph_info(f1.name) == extract_nodegraph_info(f2.name)
assert extract_nodegraph_info(f3.name) == extract_nodegraph_info(f2.name)
assert extract_nodegraph_info(f1.name) == extract_nodegraph_info(f3.name)
assert sm_data == kh_data
assert sm_data == kh_sm_data
assert ng_data == sm_data
assert ng_data == kh_data
assert ng_data == kh_sm_data
def test_nodegraph_expected_collisions():
ng_file = utils.get_test_data(".sbt.v3/internal.0")
sourmash_ng = Nodegraph.load(ng_file)
assert calc_expected_collisions(sourmash_ng) == 3.412442571740036e-07
def test_nodegraph_expected_collisions_error():
ng_file = utils.get_test_data(".sbt.v3/internal.0")
sourmash_ng = Nodegraph.load(ng_file)
with pytest.raises(SystemExit):
calc_expected_collisions(sourmash_ng, max_false_pos=1e-8)
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