feat: add penalty weights for pick_hyb_probe task

Author: emmcauley

prymer/primer3/primer3_weights.py

@@ -32,7 +32,7 @@
 @dataclass(frozen=True, init=True, slots=True)
 class Primer3Weights:
     """Holds the weights that Primer3 uses to adjust penalties
-     that originate from the designed primer(s).
+     that originate from the designed oligo(s).
 
     The weights that Primer3 uses when a parameter is less than optimal are labeled with "_lt".
     "_gt" weights are penalties applied when a parameter is greater than optimal.
@@ -42,10 +42,10 @@ class Primer3Weights:
 
      Example:
          >>> Primer3Weights() #default implementation
-         Primer3Weights(product_size_lt=1, product_size_gt=1, product_tm_lt=0.0, product_tm_gt=0.0, primer_end_stability=0.25, primer_gc_lt=0.25, primer_gc_gt=0.25, primer_self_any=0.1, primer_self_end=0.1, primer_size_lt=0.5, primer_size_gt=0.1, primer_tm_lt=1.0, primer_tm_gt=1.0)
+         Primer3Weights(product_size_lt=1, product_size_gt=1, product_tm_lt=0.0, product_tm_gt=0.0, primer_end_stability=0.25, primer_gc_lt=0.25, primer_gc_gt=0.25, primer_self_any=0.1, primer_self_end=0.1, primer_size_lt=0.5, primer_size_gt=0.1, primer_tm_lt=1.0, primer_tm_gt=1.0, probe_size_lt=0.25, probe_size_gt=0.25, probe_tm_lt=1.0, probe_tm_gt=1.0, probe_gc_lt=0.5, probe_gc_gt=0.5, probe_self_any=1.0, probe_self_end=1.0)
 
          >>> Primer3Weights(product_size_lt=5)
-         Primer3Weights(product_size_lt=5, product_size_gt=1, product_tm_lt=0.0, product_tm_gt=0.0, primer_end_stability=0.25, primer_gc_lt=0.25, primer_gc_gt=0.25, primer_self_any=0.1, primer_self_end=0.1, primer_size_lt=0.5, primer_size_gt=0.1, primer_tm_lt=1.0, primer_tm_gt=1.0)
+         Primer3Weights(product_size_lt=5, product_size_gt=1, product_tm_lt=0.0, product_tm_gt=0.0, primer_end_stability=0.25, primer_gc_lt=0.25, primer_gc_gt=0.25, primer_self_any=0.1, primer_self_end=0.1, primer_size_lt=0.5, primer_size_gt=0.1, primer_tm_lt=1.0, primer_tm_gt=1.0, probe_size_lt=0.25, probe_size_gt=0.25, probe_tm_lt=1.0, probe_tm_gt=1.0, probe_gc_lt=0.5, probe_gc_gt=0.5, probe_self_any=1.0, probe_self_end=1.0)
     """  # noqa: E501
 
     product_size_lt: int = 1
@@ -61,6 +61,14 @@ class Primer3Weights:
     primer_size_gt: float = 0.1
     primer_tm_lt: float = 1.0
     primer_tm_gt: float = 1.0
+    probe_size_lt: float = 0.25
+    probe_size_gt: float = 0.25
+    probe_tm_lt: float = 1.0
+    probe_tm_gt: float = 1.0
+    probe_gc_lt: float = 0.5
+    probe_gc_gt: float = 0.5
+    probe_self_any: float = 1.0
+    probe_self_end: float = 1.0
 
     def to_input_tags(self) -> dict[Primer3InputTag, Any]:
         """Maps weights to Primer3InputTag to feed directly into Primer3."""
@@ -78,5 +86,13 @@ def to_input_tags(self) -> dict[Primer3InputTag, Any]:
             Primer3InputTag.PRIMER_WT_SIZE_GT: self.primer_size_gt,
             Primer3InputTag.PRIMER_WT_TM_LT: self.primer_tm_lt,
             Primer3InputTag.PRIMER_WT_TM_GT: self.primer_tm_gt,
+            Primer3InputTag.PRIMER_INTERNAL_WT_SIZE_LT: self.probe_size_lt,
+            Primer3InputTag.PRIMER_INTERNAL_WT_SIZE_GT: self.probe_size_gt,
+            Primer3InputTag.PRIMER_INTERNAL_WT_TM_LT: self.probe_tm_lt,
+            Primer3InputTag.PRIMER_INTERNAL_WT_TM_GT: self.probe_tm_gt,
+            Primer3InputTag.PRIMER_INTERNAL_WT_GC_PERCENT_LT: self.probe_gc_lt,
+            Primer3InputTag.PRIMER_INTERNAL_WT_GC_PERCENT_GT: self.probe_gc_gt,
+            Primer3InputTag.PRIMER_INTERNAL_WT_SELF_ANY: self.probe_self_any,
+            Primer3InputTag.PRIMER_INTERNAL_WT_SELF_END: self.probe_self_end,
         }
         return mapped_dict

tests/primer3/test_primer3_weights.py

@@ -19,7 +19,15 @@ def test_primer_weights_valid() -> None:
     assert test_dict[Primer3InputTag.PRIMER_WT_SIZE_GT] == 0.1
     assert test_dict[Primer3InputTag.PRIMER_WT_TM_LT] == 1.0
     assert test_dict[Primer3InputTag.PRIMER_WT_TM_GT] == 1.0
-    assert len((test_dict.values())) == 13
+    assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_SIZE_LT] == 0.25
+    assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_SIZE_GT] == 0.25
+    assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_TM_LT] == 1.0
+    assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_TM_GT] == 1.0
+    assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_GC_PERCENT_LT] == 0.5
+    assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_GC_PERCENT_GT] == 0.5
+    assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_SELF_ANY] == 1.0
+    assert test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_SELF_END] == 1.0
+    assert len((test_dict.values())) == 21
 
 
 def test_primer_weights_to_input_tags() -> None: