Add test cases for find_indels_substitutions

tests/unit_tests/test_CRISPRessoCOREResources.py

@@ -0,0 +1,82 @@
+from CRISPResso2 import CRISPRessoCOREResources
+
+def test_find_indels_substitutions():
+    # no insertion or deletion
+    payload = CRISPRessoCOREResources.find_indels_substitutions(
+        'CATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAG',
+        'CATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAG',
+        [18, 19],
+    )
+    assert payload['insertion_n'] == 0
+    assert payload['deletion_n'] == 0
+    assert payload['substitution_n'] == 0
+
+    # deletion outside of quantification window
+    payload = CRISPRessoCOREResources.find_indels_substitutions(
+        'CATGGAATCCCTTCTGCA---CCTGGATCGCTTTTCCGAG',
+        'CATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAG',
+        [21, 22],
+    )
+    assert payload['insertion_n'] == 0
+    assert payload['substitution_n'] == 0
+    assert payload['deletion_n'] == 0
+
+    # deletion overlap quantification window
+    payload = CRISPRessoCOREResources.find_indels_substitutions(
+        'CATGGAATCCCTTCTGCA---CCTGGATCGCTTTTCCGAG',
+        'CATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAG',
+        [18, 19],
+    )
+    assert payload['insertion_n'] == 0
+    assert payload['substitution_n'] == 0
+    assert payload['deletion_n'] == 3
+    assert payload['all_deletion_positions'] == [18, 19, 20]
+    assert payload['deletion_positions'] == [18, 19, 20]
+    assert payload['deletion_coordinates'] == [(18, 21)]
+
+    # insertion outside of quantification window
+    payload = CRISPRessoCOREResources.find_indels_substitutions(
+        'CATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAG',
+        'CATGGAATCCCTTCTGCA---CCTGGATCGCTTTTCCGAG',
+        [21, 22],
+    )
+    assert payload['insertion_n'] == 0
+    assert payload['substitution_n'] == 0
+    assert payload['deletion_n'] == 0
+
+    # insertion overlap quantification window
+    payload = CRISPRessoCOREResources.find_indels_substitutions(
+        'CATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAG',
+        'CATGGAATCCCTTCTGCA---CCTGGATCGCTTTTCCGAG',
+        [18, 19],
+    )
+    assert payload['insertion_n'] == 0
+    assert payload['all_insertion_positions'] == [17, 18]
+    assert payload['all_insertion_left_positions'] == [17]
+    assert payload['deletion_n'] == 0
+    assert payload['substitution_n'] == 0
+
+    # deletion at ends
+    payload = CRISPRessoCOREResources.find_indels_substitutions(
+        '---GGAATCCCTTCTGCAGCACCTGGATCGCTTTTC----',
+        'CATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAG',
+        [18, 19],
+    )
+    assert payload['insertion_n'] == 0
+    assert payload['deletion_n'] == 0
+    assert payload['substitution_n'] == 0
+
+    # insertion at ends
+    payload = CRISPRessoCOREResources.find_indels_substitutions(
+        'CATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAG',
+        '----GAATCCCTTCTGCAGCACCTGGATCGCTTTTC----',
+        [18, 19],
+    )
+    assert payload['insertion_n'] == 0
+    assert payload['deletion_n'] == 0
+    assert payload['substitution_n'] == 0
+
+
+if __name__ == "__main__":
+# execute only if run as a script
+    test_find_indels_substitutions()