Bug fixes and enhancements

[GavinHuttley]

Summary by Sourcery

Add the ability to specify reference coordinates when retrieving homologs.

New Features:

• Allow users to specify a list of chromosome/scaffold names to limit the homolog search.

Tests:

• Added tests to verify that the homolog retrieval respects the specified coordinates.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request introduces a new feature to filter homologs by coordinate names and fixes a bug in the test suite.

Sequence diagram for homolog filtering by coordinate names

sequenceDiagram
    participant User
    participant CLI
    participant Genome
    participant AnnotationDB

    User->>CLI: homologs command with coord_names
    CLI->>CLI: _get_coord_names()
    Note over CLI: Parse coord_names from file or comma-separated list
    CLI->>Genome: get_ids_for_biotype()
    Genome->>AnnotationDB: get_ids_for_biotype()
    Note over AnnotationDB: Filter genes by biotype and seqid
    AnnotationDB-->>Genome: filtered gene IDs
    Genome-->>CLI: filtered gene IDs
    CLI-->>User: filtered homolog results

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Class diagram showing updated Genome and AnnotationDB methods

classDiagram
    class Genome {
        +get_ids_for_biotype(biotype: str, seqid: str|list[str], limit: int) Iterator[str]
        +get_features(biotype: str, seqid: str, name: str, start: int, stop: int, limit: int) Iterator[Feature]
    }

    class AnnotationDB {
        +get_features_matching(stable_id: str, description: str, limit: int)
        +genes: GeneData
    }

    Genome --> AnnotationDB
    note for Genome "Modified to support filtering by seqid"
    note for AnnotationDB "Updated feature matching logic"

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File-Level Changes

Change	Details	Files
Added support for filtering homologs by coordinate names.	Added a new --coord_names option to the homologs command. Implemented a function to parse coordinate names from a comma-separated string or a file. Modified the get_ids_for_biotype method in the Genome class to filter by coordinate names. Updated the get_features_matching method in the AnnotationDb class to use stable_id instead of name. Added a new test case for the homologs command with coordinate names. Added a new test case for the get_ids_for_biotype method with coordinate names.	src/ensembl_tui/cli.py src/ensembl_tui/_genome.py tests/test_cli.py tests/test_genome.py src/ensembl_tui/_annotation.py
Fixed a bug in the test suite.	Modified the test_homologs test case to use a temporary directory.	tests/test_cli.py

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[sourcery-ai]

Hey @GavinHuttley - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟡 General issues: 1 issue found
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[coveralls]

Pull Request Test Coverage Report for Build 13065303803

Details

• 14 of 17 (82.35%) changed or added relevant lines in 3 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage decreased (-0.04%) to 87.651%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/ensembl_tui/cli.py	9	10	90.0%
src/ensembl_tui/_genome.py	4	6	66.67%

Totals
Change from base Build 13022873967:	-0.04%
Covered Lines:	2605
Relevant Lines:	2972

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💛 - Coveralls