feat: add penalty weights for pick_hyb_probe task

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

@@ -1,10 +1,11 @@
 from prymer.primer3.primer3_input_tag import Primer3InputTag
-from prymer.primer3.primer3_weights import Primer3Weights
+from prymer.primer3.primer3_weights import PrimerAndAmpliconWeights
+from prymer.primer3.primer3_weights import ProbeWeights
 
 
 def test_primer_weights_valid() -> None:
- """Test instantiation of Primer3Weights object with valid input"""
- test_weights = Primer3Weights()
+ """Test instantiation of `PrimerAndAmpliconWeights` object with valid input"""
+ test_weights = PrimerAndAmpliconWeights()
  test_dict = test_weights.to_input_tags()
  assert test_dict[Primer3InputTag.PRIMER_PAIR_WT_PRODUCT_SIZE_LT] == 1
  assert test_dict[Primer3InputTag.PRIMER_PAIR_WT_PRODUCT_SIZE_GT] == 1
@@ -22,9 +23,24 @@ def test_primer_weights_valid() -> None:
  assert len((test_dict.values())) == 13
 
 
+def test_probe_weights_valid() -> None:
+ test_weights = ProbeWeights()
+ test_dict = test_weights.to_input_tags()
+ 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())) == 9
+
+
 def test_primer_weights_to_input_tags() -> None:
  """Test results from to_input_tags() with and without default values"""
- default_map = Primer3Weights().to_input_tags()
+ default_map = PrimerAndAmpliconWeights().to_input_tags()
  assert default_map[Primer3InputTag.PRIMER_PAIR_WT_PRODUCT_SIZE_LT] == 1
- customized_map = Primer3Weights(product_size_lt=5).to_input_tags()
+ customized_map = PrimerAndAmpliconWeights(product_size_lt=5).to_input_tags()
  assert customized_map[Primer3InputTag.PRIMER_PAIR_WT_PRODUCT_SIZE_LT] == 5