feat: add penalty weights for pick_hyb_probe task #28
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Codecov ReportAll modified and coverable lines are covered by tests ✅
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## em_feat_pick_hyb_probe #28 +/- ##
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+ Coverage 97.37% 97.39% +0.02%
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Files 25 25
Lines 1597 1614 +17
Branches 302 303 +1
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msto
approved these changes
Sep 25, 2024
prymer/primer3/primer3_input.py
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| @@ -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(), | |||
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issue Check that this is not None just like with probe_weights
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(I am surprised that mypy does not catch this!)
prymer/primer3/primer3_input.py
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| primer_weights: Optional[PrimerAndAmpliconWeights] = PrimerAndAmpliconWeights() | ||
| probe_weights: Optional[ProbeWeights] = None |
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note Per discussion, #48 adds validation of the presence of required weights, based on the specified task.
prymer/primer3/primer3_weights.py
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| """Holds the weights that Primer3 uses to adjust penalties | ||
| that originate from the designed primer(s). | ||
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| 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. | ||
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| Some of these settings depart from the default settings enumerated in the Primer3 manual. |
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Suggested change
| Some of these settings depart from the default settings enumerated in the Primer3 manual. | |
| Most of these settings depart from the default settings enumerated in the Primer3 manual. |
suggestion Open an issue, to enumerate the differences (and possibly the rationale?)
prymer/primer3/primer3_weights.py
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| """Holds the weights that Primer3 uses to adjust penalties | ||
| that originate from the designed internal probe(s).""" |
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doc Make the summary line one line, and add an Attributes block
https://google.github.io/styleguide/pyguide.html#384-classes
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Part of #11 . This PR adds
PRIMER_INTERNAL_WT_*fields to aProbeWeightsdataclass that now exists alongside aPrimerAndAmpliconWeightsclass. Similar to thePRIMER_weights, the size, melting temperature, GC content, and complementarity of the probe are penalized. Defaults for the dataclass were chosen to heavily weight against probe complementarity and out-of-range melting temperature and apply a smaller penalty to out-of-spec GC content and probe size.ProbeWeightsis separate fromPrimerAndAmpliconWeightsto maintain separation of tasks and clarity.