feat: add penalty weights for pick_hyb_probe task #28
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
emmcauley
force-pushed
the
em_add_hyb_probe_weights
branch
4 times, most recently
from
a47953e to
9dd4ebb
Compare
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## em_feat_pick_hyb_probe #28 +/- ##
==========================================================
+ Coverage 97.37% 97.39% +0.02%
==========================================================
Files 25 25
Lines 1597 1614 +17
Branches 302 303 +1
==========================================================
+ Hits 1555 1572 +17
Misses 23 23
Partials 19 19 ☔ View full report in Codecov by Sentry. |
emmcauley
force-pushed
the
em_add_hyb_probe_weights
branch
from
9dd4ebb to
54b30a3
Compare
emmcauley
force-pushed
the
em_add_hyb_probe_weights
branch
from
54b30a3 to
8275f3d
Compare
emmcauley
force-pushed
the
em_add_hyb_probe_weights
branch
from
48f19af to
8275f3d
Compare
msto
approved these changes
Sep 25, 2024
prymer/primer3/primer3_input.py
Outdated
| @@ -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(), | |||
There was a problem hiding this comment.
issue Check that this is not None just like with probe_weights
There was a problem hiding this comment.
(I am surprised that mypy does not catch this!)
prymer/primer3/primer3_input.py
Outdated
Comment on lines
103
to
104
| primer_weights: Optional[PrimerAndAmpliconWeights] = PrimerAndAmpliconWeights() | ||
| probe_weights: Optional[ProbeWeights] = None |
There was a problem hiding this comment.
note Per discussion, #48 adds validation of the presence of required weights, based on the specified task.
prymer/primer3/primer3_weights.py
Outdated
| """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. |
There was a problem hiding this comment.
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
Outdated
Comment on lines
90
to
91
| """Holds the weights that Primer3 uses to adjust penalties | ||
| that originate from the designed internal probe(s).""" |
There was a problem hiding this comment.
doc Make the summary line one line, and add an Attributes block
https://google.github.io/styleguide/pyguide.html#384-classes
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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.