Expose generate_alignment + generate_hgvs_variants_from_alignment functions #18
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README.md
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Minor typo, provides → provide
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boolean flags for strategies are not my favorite, could a separate method make a better API? Or perhaps allow the strategy to be passed in?
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This is existing functionality that is just getting moved so it would be a breaking change to get rid of the flag. Don't think it's worth doing right now, but I am open to a change in a follow up PR if you feel its important. Personally I find the ergonomics of passing a boolean to be a bit better then some string that represents the "method" you want (we'd likely want some kind of constant / enum, etc). If there were a bunch of methods it would make more sense.
palamedes/__init__.py
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| """ | ||
| Given a pairwise alignment object and a molecule type, generate a list of HGVS SequenceVariants. | ||
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| - Alignment: Generated via BioPython.PairwiseAligner - (`generate_alignment` for more information) |
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"See generate_alignemt for more information"
palamedes/__init__.py
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Can you trim this excess white space?
| def generate_hgvs_variants_from_alignment( | ||
| alignment: Alignment, use_non_standard_substitution_rules: bool = False, molecule_type: str = MOLECULE_TYPE_PROTEIN | ||
| ) -> list[SequenceVariant]: | ||
| """ |
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Adding some examples here using the follow format might be nice for the API docs:
.. code-block:: python
>>> from palamedes import generate_hgvs_variants
>>> generate_hgvs_variants("PFKISIHL", "TPFKISIH")
[
SequenceVariant(ac=ref, type=p, posedit=Pro1extThr-1, gene=None),
SequenceVariant(ac=ref, type=p, posedit=Leu8del, gene=None),
]
This is from the doc string for generate_hgvs_variants
| molecule_type: str = MOLECULE_TYPE_PROTEIN, | ||
| aligner: PairwiseAligner | None = None, | ||
| ) -> Alignment: | ||
| """ |
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Since this is public now, can you add some code example to the doc string, using the same block as above?
| raise NotImplementedError( | ||
| f"Type {molecule_type} unsupported or unrecognized! Current supported types: {','.join(BUILDER_CONFIG.keys())}" | ||
| ) |
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Thank you for making this error message better!
palamedes/test_palamedes.py
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| @@ -0,0 +1,216 @@ | |||
| from palamedes import generate_variant_blocks, generate_alignment | |||
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generate_variant_blocks is still defined in align.py, so the tests for it should stay in there. Only generate_alignment was moved.
Description
As part of the alignment work, we are exposing some additional functions that can be used externally.
Also, as part of this PR
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