Implement ORF searcher with corrected terminal translation

[ShinThomas]

Summary

Implements the V2 ORF searcher for issue #17. The component accepts DNA and returns candidate protein sequences for downstream domain scanning.

Corrects a truncation bug in orffinder==1.8 that can drop the last complete codon from incomplete terminal ORFs.

Changes

• Added OrffinderOrfSearcher, preserving OrfSearcherTemplate.
• Uses orffinder.getORFs() to locate candidates, then extracts and translates complete codons on the appropriate strand without padding.
• Checks minimum length against the actual nucleotide span and excludes terminal stop codons from complete ORFs.
• Validates DNA inputs and configuration; supports ATG starts and the standard genetic code.
• Leaves candidate sorting and deduplication to the pipeline.
• Pins the tested dependency to orffinder==1.8.

Regression examples now produce:

• ATGAAAGGG → MKG
• ATGAAAGGGAAA → MKGK
• Reverse-strand input CCCTTTCAT → MKG

Documentation explains nucleotide-length thresholds, accepted DNA symbols, nested and trailing candidate settings, and the dependency-specific workaround.

Testing

Local checks completed in lverage-v2:

• V2 unittest discovery: 92 passed.
• Retained legacy JASPAR-window tests: 11 passed.
• Strict nitpicky Sphinx build: passed.

Tests cover both strands, incomplete suffixes with 0/1/2 leftover bases, length boundaries, ambiguity, invalid inputs, nested filtering, and protein handoff to the pipeline’s domain scanner.

[Copilot]

🟢 Approval recommended

The implementation matches the dependency’s coordinate behavior and is comprehensively tested and documented.

0 open findings

What changed in this PR

Implements the V2 ORF-search adapter with corrected terminal translation.

Changes:

• Adds validated six-frame ORF discovery and translation.
• Adds regression, configuration, and pipeline integration tests.
• Pins and documents orffinder 1.8 behavior.

File	Description
src/​lverage/​orf_searcher.py	Implements the ORF-search adapter.
tests/​v2/​test_orf_searcher.py	Adds comprehensive tests.
pyproject.toml	Adds the pinned dependency.
docs/​api/​orf_searcher.rst	Documents behavior and limitations.
docs/​singularity_setup.md	Records the runtime dependency.

🧠 Review effort: Balanced

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