Merge branch 'main' into #67-training-doesnt-like-sig-files

.gitignore

@@ -167,3 +167,4 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+gtdb-rs214-reps.k31_0.9995_pretrained/

tests/test_y_integration_tests.py

@@ -89,4 +89,16 @@ def test_run_train_sig():
         config = json.load(f)
         assert config['ksize'] == int(ksize)
         assert config['ani_thresh'] == float(ani_thresh)
+
+def test_run_pretrained_ref_db():
+    cmd = "yacht download pretrained_ref_db --database gtdb --db_version rs214 --k 31 --ani_thresh 0.9995 --outfolder ./"
+    res = subprocess.run(cmd, shell=True, check=True)
+    assert res.returncode == 0
+
+def test_run_yacht_pretrained_ref_db():
+    cmd = "yacht run --json ./gtdb-rs214-reps.k31_0.9995_pretrained/gtdb-rs214-reps.k31_0.9995_config.json --sample_file tests/testdata/sample.sig.zip --significance 0.99 --num_threads 32 --min_coverage_list 1 0.6 0.2 0.1 --out ./result_pretrained.xlsx"
+    res = subprocess.run(cmd, shell=True, check=True)
+    assert res.returncode == 0
+
+    assert exists('result_pretrained.xlsx')