feat: add penalty weights for pick_hyb_probe task

Author: emmcauley

prymer/primer3/primer3_input.py

@@ -8,12 +8,14 @@
 The module uses:
 
 1. [`Primer3Parameters`][prymer.primer3.primer3_parameters.Primer3Parameters]
-to specify user-specified criteria for primer design
-2. [`Primer3Weights`][prymer.primer3.primer3_weights.Primer3Weights] to establish penalties
-based on those criteria
-3. [`Primer3Task`][prymer.primer3.primer3_task.Primer3Task] to organize task-specific
+    to specify user-specified criteria for primer design
+2. [`PrimerAndAmpliconWeights`][prymer.primer3.primer3_weights.PrimerAndAmpliconWeights]
+    to establish penalties based on those criteria
+3. [`ProbeWeights`][prymer.primer3.primer3_weights.ProbeWeights] to specify penalties based on probe
+    design criteria
+4. [`Primer3Task`][prymer.primer3.primer3_task.Primer3Task] to organize task-specific
     logic.
-4. [`Span`](index.md#prymer.api.span.Span] to specify the target region.
+5. [`Span`](index.md#prymer.api.span.Span] to specify the target region.
 
 The `Primer3Input.to_input_tags(]` method
 The main purpose of this class is to generate the
@@ -81,12 +83,14 @@
 
 from dataclasses import dataclass
 from typing import Any
+from typing import Optional
 
 from prymer.api.span import Span
 from prymer.primer3.primer3_input_tag import Primer3InputTag
 from prymer.primer3.primer3_parameters import Primer3Parameters
 from prymer.primer3.primer3_task import Primer3TaskType
-from prymer.primer3.primer3_weights import Primer3Weights
+from prymer.primer3.primer3_weights import PrimerAndAmpliconWeights
+from prymer.primer3.primer3_weights import ProbeWeights
 
 
 @dataclass(frozen=True, init=True, slots=True)
@@ -96,7 +100,8 @@ class Primer3Input:
     target: Span
     task: Primer3TaskType
     params: Primer3Parameters
-    weights: Primer3Weights = Primer3Weights()
+    primer_weights: Optional[PrimerAndAmpliconWeights] = PrimerAndAmpliconWeights()
+    probe_weights: Optional[ProbeWeights] = None
 
     def to_input_tags(self, design_region: Span) -> dict[Primer3InputTag, Any]:
         """Assembles `Primer3InputTag` and values for input to `Primer3`
@@ -116,6 +121,7 @@ def to_input_tags(self, design_region: Span) -> dict[Primer3InputTag, Any]:
         assembled_tags = {
             **primer3_task_params,
             **self.params.to_input_tags(),
-            **self.weights.to_input_tags(),
+            **self.primer_weights.to_input_tags(),
+            **(self.probe_weights.to_input_tags() if self.probe_weights is not None else {}),
         }
         return assembled_tags

prymer/primer3/primer3_weights.py

@@ -15,9 +15,9 @@
 
 
 ```python
->>> Primer3Weights(product_size_lt=1, product_size_gt=1)
+>>> PrimerAndAmpliconWeights(product_size_lt=1, product_size_gt=1)
 Primer3Weights(product_size_lt=1, product_size_gt=1, ...)
->>> Primer3Weights(product_size_lt=5, product_size_gt=1)
+>>> PrimerAndAmpliconWeights(product_size_lt=5, product_size_gt=1)
 Primer3Weights(product_size_lt=5, product_size_gt=1, ...)
 
 ```
@@ -30,22 +30,23 @@
 
 
 @dataclass(frozen=True, init=True, slots=True)
-class Primer3Weights:
+class PrimerAndAmpliconWeights:
     """Holds the weights that Primer3 uses to adjust penalties
      that originate from the designed primer(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.
 
+    Some of these settings depart from the default settings enumerated in the Primer3 manual.
     Please see the Primer3 manual for additional details:
      https://primer3.org/manual.html#globalTags
 
      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)
+         >>> PrimerAndAmpliconWeights() #default implementation
+         PrimerAndAmpliconWeights(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)
+         >>> PrimerAndAmpliconWeights(product_size_lt=5)
+         PrimerAndAmpliconWeights(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
@@ -80,3 +81,34 @@ def to_input_tags(self) -> dict[Primer3InputTag, Any]:
             Primer3InputTag.PRIMER_WT_TM_GT: self.primer_tm_gt,
         }
         return mapped_dict
+
+
+@dataclass(frozen=True, init=True, slots=True)
+class ProbeWeights:
+    """Holds the weights that Primer3 uses to adjust penalties
+    that originate from the designed internal probe(s)."""
+
+    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
+    probe_hairpin_th: float = 1.0
+
+    def to_input_tags(self) -> dict[Primer3InputTag, Any]:
+        """Maps weights to Primer3InputTag to feed directly into Primer3."""
+        mapped_dict = {
+            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,
+            Primer3InputTag.PRIMER_INTERNAL_WT_HAIRPIN_TH: self.probe_hairpin_th,
+        }
+        return mapped_dict

tests/primer3/test_primer3_weights.py

@@ -19,7 +19,16 @@ 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 test_dict[Primer3InputTag.PRIMER_INTERNAL_WT_HAIRPIN_TH] == 1.0
+    assert len((test_dict.values())) == 22
 
 
 def test_primer_weights_to_input_tags() -> None: