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import pytest
import sourmash
import sourmash_tst_utils as utils
from sourmash.sourmash_args import load_one_signature, SaveSignaturesToLocation
@utils.in_tempdir
def test_sourmash_signature_api(c):
e = sourmash.MinHash(n=1, ksize=20)
sig = sourmash.SourmashSignature(e)
with SaveSignaturesToLocation(c.output("xxx.sig")) as save_sigs:
save_sigs.add(sig)
sig_x1 = load_one_signature(c.output("xxx.sig"))
sig_x2 = list(sourmash.load_file_as_signatures(c.output("xxx.sig")))[0]
assert sig_x1 == sig
assert sig_x2 == sig
@utils.in_tempdir
def test_load_index_0_no_file(c):
with pytest.raises(ValueError) as exc:
sourmash.load_file_as_index(c.output("does-not-exist"))
assert "Error while reading signatures from " in str(exc.value)
def test_load_index_1():
testfile = utils.get_test_data("prot/protein.sbt.zip")
idx = sourmash.load_file_as_index(testfile)
sigs = list(idx.signatures())
assert len(sigs) == 2
def test_load_index_2():
testfile = utils.get_test_data("prot/protein.lca.json.gz")
idx = sourmash.load_file_as_index(testfile)
sigs = list(idx.signatures())
assert len(sigs) == 2
def test_load_index_3():
testfile = utils.get_test_data("prot/protein/")
idx = sourmash.load_file_as_index(testfile)
sigs = list(idx.signatures())
assert len(sigs) == 2
def test_load_index_4():
testfile = utils.get_test_data("prot/all.zip")
idx = sourmash.load_file_as_index(testfile)
sigs = list(idx.signatures())
assert len(sigs) == 8
def test_load_index_4_b():
testfile = utils.get_test_data("prot/protein.zip")
idx = sourmash.load_file_as_index(testfile)
sigs = list(idx.signatures())
assert len(sigs) == 2
def test_load_fasta_as_signature():
# try loading a fasta file - should fail with informative exception
testfile = utils.get_test_data("short.fa")
with pytest.raises(Exception) as exc:
sourmash.load_file_as_index(testfile)
print(exc.value)
assert (
f"Error while reading signatures from '{testfile}' - got sequences instead! Is this a FASTA/FASTQ file?"
in str(exc.value)
)
def test_load_and_search_sbt_api():
treefile = utils.get_test_data("prot/protein.sbt.zip")
queryfile = utils.get_test_data(
"prot/protein/GCA_001593925.1_ASM159392v1_protein.faa.gz.sig"
)
tree = sourmash.load_file_as_index(treefile)
query = load_one_signature(queryfile)
results = list(tree.search(query, threshold=0))
assert len(results) == 2
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