Merge Primer*Weights into Primer3Parameters, remove Primer3Input #112
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tfenne
reviewed
Jan 15, 2025
prymer/primer3/primer3.py
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| ): # if the right primer has too many dinucleotide bases, fail it | ||
| dinuc_pair_failures.append(primer_pair.right_primer) | ||
| valid = False | ||
| if valid: # if neither failed, append the pair to a list of valid designs | ||
| valid_primer_pair_designs.append(primer_pair) | ||
| return valid_primer_pair_designs, dinuc_pair_failures | ||
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| def design(self, design_input: Primer3Input) -> Primer3Result: # noqa: C901 | ||
| def design(self, design_input: Primer3Parameters) -> Primer3Result: # noqa: C901 |
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I think this would need to take:
amplicon_parameters: AmpliconParameters | None, probe_parameter: ProbeParameters | NoneWhat you have works for the current set of use cases, but one primer3 task we haven't implemented yet supports designing primer pairs and probes concurrently, and then you need both sets of parameters.
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I leave it for now, and we can decide later if we want to have two parameters to design, or to create a third parameters class:
class AmpliconAndProbeParameters(Primer3Parameters):
amplicon_params: AmpliconParams
probe_params: ProbeParams
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## dev #112 +/- ##
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- Coverage 97.37% 96.95% -0.42%
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Files 20 18 -2
Lines 1635 1575 -60
Branches 188 184 -4
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- Hits 1592 1527 -65
- Misses 24 27 +3
- Partials 19 21 +2 ☔ View full report in Codecov by Sentry. |
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nh13
changed the title
nh13
commented
Jan 16, 2025
| @@ -731,29 +754,3 @@ def _check_design_results(design_input: Primer3Input, design_results: dict[str, | |||
| count: int = int(maybe_count) | |||
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| return count | |||
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| def _has_acceptable_dinuc_run(design_input: Primer3Input, oligo_design: Oligo) -> bool: | |||
tfenne
approved these changes
Jan 17, 2025
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Primer*Weightsclasses into their corresponding amplicon and probe parameter classes (reduces 4 classes to two). The attributes have the_wtsuffix in their name. Theprimer3.primer3.primer3_weightsmodule is gone.Primer3Inputfunctionality intoPrimer3directly.primer3.primer3.primer3_inputis now gone.WeightRangefor the weights when a value is out of range (either less than, or greater than). Could use a better name?Primer3.designnow explicitly takes in the design task and target, in addition to the params. It checks to make sure that the task (e.g. design left primers) matches the params (e.g. amplicons).Primer3Task(remove methods no longer used)