Generalised recombinase functionality

[manulera]

Closes #435 and completes #496

cc @BjornFJohansson please have a look at the docs of the new module here

It works for attB / attP - like recombinases, but perhaps I am missing something

[codecov]

Codecov Report

❌ Patch coverage is 97.17514% with 5 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/pydna/opencloning_models.py	76.92%	2 Missing and 1 partial ⚠️
src/pydna/recombinase.py	98.33%	2 Missing ⚠️

@@            Coverage Diff             @@
##           master     #564      +/-   ##
==========================================
+ Coverage   93.56%   93.75%   +0.18%     
==========================================
  Files          37       38       +1     
  Lines        5302     5424     +122     
  Branches      748      763      +15     
==========================================
+ Hits         4961     5085     +124     
+ Misses        267      265       -2     
  Partials       74       74              

Files with missing lines	Coverage Δ
src/pydna/assembly2.py	97.41% <100.00%> (+0.04%)	⬆️
src/pydna/gateway.py	100.00% <100.00%> (+12.06%)	⬆️
src/pydna/recombinase.py	98.33% <98.33%> (ø)
src/pydna/opencloning_models.py	97.66% <76.92%> (-0.94%)	⬇️

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[Copilot]

Pull request overview

This pull request implements generalized recombinase functionality for pydna, addressing issue #435 and building upon PR #496. The changes introduce a new recombinase module that provides a flexible framework for simulating site-specific recombination reactions, and refactors the existing Gateway cloning functionality to use this new module.

Changes:

• Added new src/pydna/recombinase.py module with Recombinase and RecombinaseCollection classes for generic recombinase operations
• Refactored src/pydna/gateway.py to use the new recombinase infrastructure, converting site definitions to use lowercase notation for homology cores
• Added recombinase_integration() and recombinase_excision() functions to src/pydna/assembly2.py
• Added comprehensive test suite in tests/test_module_recombinase.py covering various scenarios
• Added RecombinaseSource class to src/pydna/opencloning_models.py for provenance tracking
• Updated test expectations in tests/test_module_assembly2.py to reflect new site ordering behavior

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
src/pydna/recombinase.py	New module implementing generic recombinase functionality with support for site finding, annotation, and overlap detection
src/pydna/gateway.py	Refactored to use new Recombinase classes, simplified by delegating to RecombinaseCollection
src/pydna/assembly2.py	Added recombinase_integration and recombinase_excision functions, plus minor fixes to SingleFragmentAssembly
src/pydna/opencloning_models.py	Added RecombinaseSource class for tracking recombinase-based assemblies
tests/test_module_recombinase.py	Comprehensive test suite for the new recombinase module
tests/test_module_assembly2.py	Updated expected error message to reflect new site ordering

Comments suppressed due to low confidence (3)

src/pydna/assembly2.py:1974

• The comment states "Remove matches where the whole sequence matches", but this filtering removes matches where the match length equals the fragment length. For recombinase reactions, this makes sense (you don't want the entire sequence to match itself), but it's worth noting this is a semantic change from the previous behavior. Consider adding a more detailed comment explaining why full-length matches need to be filtered out for recombinase assembly, as this might not be immediately obvious to future maintainers.

        # Remove matches where the whole sequence matches
        matches = [match for match in matches if match[2] != len(frag)]

src/pydna/recombinase.py:140

• Missing space in error message. Should be "Recombinase recognition site is not in the expected format. Expected format:" with a space before "Expected".

        raise ValueError(
            "Recombinase recognition site is not in the expected format."
            "Expected format: [A-Z]+[a-z]+[A-Z]+, e.g. 'ATGCCCTAAaaTT'"
        )

src/pydna/recombinase.py:189

• Missing space in error message. Should be "Recombinase recognition sites do not have matching homology cores. Expected" with a space before "Expected".

            raise ValueError(
                "Recombinase recognition sites do not have matching homology cores."
                f"Expected {site1[off1:off1 + len1]} == {site2[off2:off2 + len2]}"
            )

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[manulera]

Hey @BjornFJohansson I am merging this, as it does not touch existing code, and I need to make a separate PR to have the latest biopython.