added a few tests

tests/test_utils.py

@@ -8,6 +8,14 @@
 sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 from srcs import utils
 import sourmash
+import unittest
+import math
+import json
+import pytest
+import tempfile
+import gzip
+import sys
+import shutil
 
 
 def to_testing_data(file):
@@ -53,9 +61,104 @@
     assert type(sig) == sourmash.signature.FrozenSourmashSignature
     assert sig.jaccard(sig) == 1.0
 
+class TestGetColumnIndices(unittest.TestCase):
+    def test_1(self):
+        column_name_to_index = {
+            "TAXID": 1,
+            "RANK": 0,
+            "PERCENTAGE": 2,
+            "TAXPATH": 3,
+            "TAXPATHSN": 4
+        }
+        indices = utils.get_column_indices(column_name_to_index)
+        assert indices == (0, 1, 2, 3, 4)
+
+    def test_2(self):
+        column_name_to_index = {
+            "RANK": 0,
+            "PERCENTAGE": 2,
+            "TAXPATH": 3,
+            "TAXPATHSN": 4
+        }
+        with self.assertRaises(RuntimeError):
+            indices = utils.get_column_indices(column_name_to_index)
+
+    def test_3(self):
+        column_name_to_index = {
+            "TAXID": 1,
+            "PERCENTAGE": 2,
+            "TAXPATH": 3,
+            "TAXPATHSN": 4
+        }
+        with self.assertRaises(RuntimeError):
+            indices = utils.get_column_indices(column_name_to_index)
+
+    def test_4(self):
+        column_name_to_index = {
+            "TAXID": 1,
+            "RANK": 0,
+            "TAXPATH": 3,
+            "TAXPATHSN": 4
+        }
+        with self.assertRaises(RuntimeError):
+            indices = utils.get_column_indices(column_name_to_index)
+
+    def test_5(self):
+        column_name_to_index = {
+            "TAXID": 1,
+            "RANK": 0,
+            "PERCENTAGE": 2,
+            "TAXPATHSN": 4
+        }
+        with self.assertRaises(RuntimeError):
+            indices = utils.get_column_indices(column_name_to_index)
+
+    def test_6(self):
+        column_name_to_index = {
+            "TAXID": 1,
+            "RANK": 0,
+            "PERCENTAGE": 2,
+            "TAXPATH": 3
+        }
+        indices = utils.get_column_indices(column_name_to_index)
+        assert indices[4] is None
+
+class TestGetCamiProfile(unittest.TestCase):
+    def test_1(self):
+        file_path = os.path.join(os.path.dirname(__file__), 'testdata/sample_cami.txt')
+        with open(file_path, 'r') as file:
+            sample_cami_content = file.readlines()
+
+        profiles = utils.get_cami_profile(sample_cami_content)
 
+        expected_header = {
+            'SAMPLEID': 'CAMI_LOW_S001',
+            'VERSION': '0.9.1',
+            'RANKS': 'superkingdom|phylum|class|order|family|genus|species|strain',
+            'TAXONOMYID': 'ncbi-taxonomy_DATE',
+            '__PROGRAM__': 'unknown'
+        }
 
+        assert len(profiles) == 1
+        sample_id, header, profile = profiles[0]
 
+        assert sample_id == "CAMI_LOW_S001"
+        assert header == expected_header
+        assert len(profile) == 2044
 
+        prediction1 = profile[0]
+        assert prediction1.rank == 'superkingdom'
+        assert prediction1.taxid == '2157'
+        assert math.isclose(prediction1.percentage, 0.029528, abs_tol=1e-6)
+        assert prediction1.taxpath == '2157'
+        assert prediction1.taxpathsn == 'Archaea'
 
+        prediction2 = profile[1]
+        assert prediction2.rank == 'superkingdom'
+        assert prediction2.taxid == '2'
+        assert math.isclose(prediction2.percentage, 29.183763, rel_tol=1e-6)
+        assert prediction2.taxpath == '2'
+        assert prediction2.taxpathsn == 'Bacteria'
 
+if __name__ == '__main__':
+    unittest.main()