feat: added post init checks for max_gap_opens and max_gap_extends

prymer/offtarget/offtarget_detector.py

@@ -157,7 +157,7 @@ class OffTargetDetector(AbstractContextManager):
     alignments does not exceed the specified maximum number of primer pair hits.
     """
 
-    def __init__(
+    def __init__(  # noqa: C901
         self,
         ref: Path,
         max_primer_hits: int,
@@ -211,15 +211,13 @@ def __init__(
                 `three_prime_region_length`. Must be between 0 and `three_prime_region_length`,
                 inclusive.
             max_mismatches: the maximum number of mismatches allowed in the full length primer
-                (including any in the three prime region)
+                (including any in the three prime region). Must be greater than or equal to 0.
             max_gap_opens: the maximum number of gaps (insertions or deletions) allowable in an
-                alignment of a oligo to the reference
+                alignment of a oligo to the reference. Must be greater than or equal to 0.
             max_gap_extends: the maximum number of gap extensions allowed; extending a gap
                 beyond a single base costs 1 gap extension.  Can be set to -1 to allow
                 unlimited extensions up to max diffs (aka max mismatches), while disallowing
-                "long gaps".
-            max_amplicon_size: the maximum amplicon size to consider amplifiable
-                (including any in the three prime region). Must be greater than or equal to 0.
+                "long gaps". Must be greater than or equal to -1.
             max_amplicon_size: the maximum amplicon size to consider amplifiable. Must be greater
                 than 0.
             cache_results: if True, cache results for faster re-querying
@@ -238,6 +236,8 @@ def __init__(
             ValueError: If `max_mismatches_in_three_prime_region` is outside the range 0 to
                 `three_prime_region_length`, inclusive.
             ValueError: If `max_mismatches` is not greater than or equal to 0.
+            ValueError: If `max_gap_opens` is not greater than or equal to 0.
+            ValueError: If `max_gap_extends` is not -1 or greater than or equal to 0.
         """
         errors: list[str] = []
         if max_amplicon_size < 1:
@@ -274,6 +274,15 @@ def __init__(
             errors.append(
                 f"'max_mismatches' must be greater than or equal to 0. Saw {max_mismatches}"
             )
+        if max_gap_opens < 0:
+            errors.append(
+                f"'max_gap_opens' must be greater than or equal to 0. Saw {max_gap_opens}"
+            )
+        if max_gap_extends < -1:
+            errors.append(
+                "'max_gap_extends' must be -1 (for unlimited extensions up to 'max_mismatches'="
+                f"{max_mismatches}) or greater than or equal to 0. Saw {max_gap_extends}"
+            )
 
         if len(errors) > 0:
             raise ValueError("\n".join(errors))

tests/offtarget/test_offtarget.py

@@ -1,3 +1,4 @@
+import re
 from dataclasses import dataclass
 from pathlib import Path
 
@@ -355,17 +356,20 @@ class CustomPrimer(Oligo):
 @pytest.mark.parametrize(
     (
         "max_primer_hits,max_primer_pair_hits,min_primer_pair_hits,three_prime_region_length,"
-        "max_mismatches_in_three_prime_region,max_mismatches,max_amplicon_size,expected_error"
+        "max_mismatches_in_three_prime_region,max_mismatches,max_amplicon_size,"
+        "max_gap_opens,max_gap_extends,expected_error"
     ),
     [
-        (-1, 1, 1, 20, 0, 0, 1, "'max_primer_hits' must be greater than or equal to 0. Saw -1"),
-        (1, -1, 1, 20, 0, 0, 1, "'max_primer_pair_hits' must be greater than or equal to 0. Saw -1"),  # noqa: E501
-        (1, 1, -1, 20, 0, 0, 1, "'min_primer_pair_hits' must be greater than or equal to 0. Saw -1"),  # noqa: E501
-        (1, 1, 1, 0, 0, 0, 1, "'three_prime_region_length' must be greater than 0. Saw 0"),
-        (1, 1, 1, 20, -1, 0, 1, "'max_mismatches_in_three_prime_region' must be between 0 and 'three_prime_region_length'=20 inclusive. Saw -1"),  # noqa: E501
-        (1, 1, 1, 20, 21, 0, 1, "'max_mismatches_in_three_prime_region' must be between 0 and 'three_prime_region_length'=20 inclusive. Saw 21"),  # noqa: E501
-        (1, 1, 1, 20, 0, -1, 1, "'max_mismatches' must be greater than or equal to 0. Saw -1"),
-        (1, 1, 1, 20, 0, 0, 0, "'max_amplicon_size' must be greater than 0. Saw 0"),
+        (-1, 1, 1, 20, 0, 0, 1, 0, 0, "'max_primer_hits' must be greater than or equal to 0. Saw -1"),  # noqa: E501
+        (1, -1, 1, 20, 0, 0, 1, 0, 0, "'max_primer_pair_hits' must be greater than or equal to 0. Saw -1"),  # noqa: E501
+        (1, 1, -1, 20, 0, 0, 1, 0, 0, "'min_primer_pair_hits' must be greater than or equal to 0. Saw -1"),  # noqa: E501
+        (1, 1, 1, 0, 0, 0, 1, 0, 0, "'three_prime_region_length' must be greater than 0. Saw 0"),
+        (1, 1, 1, 20, -1, 0, 1, 0, 0, "'max_mismatches_in_three_prime_region' must be between 0 and 'three_prime_region_length'=20 inclusive. Saw -1"),  # noqa: E501
+        (1, 1, 1, 20, 21, 0, 1, 0, 0, "'max_mismatches_in_three_prime_region' must be between 0 and 'three_prime_region_length'=20 inclusive. Saw 21"),  # noqa: E501
+        (1, 1, 1, 20, 0, -1, 1, 0, 0, "'max_mismatches' must be greater than or equal to 0. Saw -1"),  # noqa: E501
+        (1, 1, 1, 20, 0, 0, 0, 0, 0, "'max_amplicon_size' must be greater than 0. Saw 0"),
+        (1, 1, 1, 20, 0, 0, 1, -1, 0, "'max_gap_opens' must be greater than or equal to 0. Saw -1"),
+        (1, 1, 1, 20, 0, 5, 1, 0, -2, re.escape("'max_gap_extends' must be -1 (for unlimited extensions up to 'max_mismatches'=5) or greater than or equal to 0. Saw -2")), #noqa: E501
     ],
 )
 # fmt: on
@@ -378,6 +382,8 @@ def test_init(
     max_mismatches_in_three_prime_region: int,
     max_mismatches: int,
     max_amplicon_size: int,
+    max_gap_opens: int,
+    max_gap_extends: int,
     expected_error: str,
 ) -> None:
     with pytest.raises(ValueError, match=expected_error):
@@ -390,4 +396,6 @@ def test_init(
             max_mismatches_in_three_prime_region=max_mismatches_in_three_prime_region,
             max_mismatches=max_mismatches,
             max_amplicon_size=max_amplicon_size,
+            max_gap_opens=max_gap_opens,
+            max_gap_extends=max_gap_extends,
         )