added assertions, fixed path

tests/integration_tests.py

@@ -22,15 +22,15 @@ def make_train_fasta():
 def test_sourmash_sketch_command():
     with tempfile.TemporaryDirectory() as tmp_dir:
         make_train_fasta()
-        
+
         fasta_file = "example.fasta"
         output_file = os.path.join(tmp_dir, "training_database.sig.zip")
         cmd = [
             "sourmash", "sketch", "dna", "-f", "-p", "k=31,scaled=1000,abund", "--singleton", fasta_file, "-o", output_file
         ]
-        
+
         subprocess.run(cmd, check=True)
-        
+
         assert os.path.isfile(output_file)
 
 def test_make_training_data_from_sketches():
@@ -63,11 +63,29 @@ def test_make_training_data_from_sketches():
         config = json.load(f)
         assert config['ksize'] == int(ksize)
         assert config['ani_thresh'] == float(ani_thresh)
-        
+
 def test_run_yacht():
     cmd = "python run_YACHT.py --json gtdb_ani_thresh_0.95_config.json --sample_file 'tests/testdata/sample.sig.zip' --significance 0.99 --min_coverage_list 1 0.6 0.2 0.1"
-    
+
     res = subprocess.run(cmd, shell=True, check=True)
     assert res.returncode == 0
 
     assert exists('result.xlsx')
+
+def test_run_yacht_and_standardizer():
+    cmd = "cd demo; sourmash sketch dna -f -p k=31,scaled=1000,abund -o sample.sig.zip query_data/query_data.fq"
+    res = subprocess.run(cmd, shell=True, check=True)
+    assert res.returncode == 0
+    cmd = "cd demo; sourmash sketch fromfile ref_paths.csv -p dna,k=31,scaled=1000,abund -o ref.sig.zip --force-output-already-exists"
+    res = subprocess.run(cmd, shell=True, check=True)
+    assert res.returncode == 0
+    cmd = "cd demo; python ../make_training_data_from_sketches.py --force --ref_file ref.sig.zip --ksize 31 --num_threads 1 --ani_thresh 0.95 --prefix 'demo_ani_thresh_0.95' --outdir ./"
+    res = subprocess.run(cmd, shell=True, check=True)
+    assert res.returncode == 0
+    cmd = "cd demo; python ../run_YACHT.py --json demo_ani_thresh_0.95_config.json --sample_file sample.sig.zip --significance 0.99 --num_threads 1 --min_coverage_list 1 0.6 0.2 0.1 --out result.xlsx"
+    res = subprocess.run(cmd, shell=True, check=True)
+    assert res.returncode == 0
+    cmd = "cd demo; python ../srcs/standardize_yacht_output.py --yacht_output result.xlsx --sheet_name min_coverage0.2 --genome_to_taxid toy_genome_to_taxid.tsv --mode cami --sample_name 'MySample' --outfile_prefix cami_result --outdir ./"
+    res = subprocess.run(cmd, shell=True, check=True)
+    assert res.returncode == 0
+    assert exists('demo/cami_result.cami')

tests/test_workflow.py

@@ -84,4 +84,4 @@ def test_demo_workflow():
     cmd = "cd demo; python ../srcs/standardize_yacht_output.py --yacht_output result.xlsx --sheet_name min_coverage0.2 --genome_to_taxid toy_genome_to_taxid.tsv --mode cami --sample_name 'MySample' --outfile_prefix cami_result --outdir ./"
     res = subprocess.run(cmd, shell=True, check=True)
     assert res.returncode == 0
-    assert exists('./cami_result.cami')
+    assert exists('demo/cami_result.cami')