Added argument to gff3_to_fasta that allows user to determine what at…

[MonicaPoelchau-USDA]

…tributes are included in the fasta defline. Model used: GPT-5.4 mini

[Copilot]

Pull request overview

This PR extends gff3_to_fasta to let users control which GFF3 attributes are included in FASTA deflines via a new CLI argument, and updates docs/tests accordingly.

Changes:

• Added -da/--defline_attributes and plumbing through script_main() → main() → extract_start_end()/splicer().
• Implemented helpers to normalize attribute lists and format selected attributes into FASTA deflines, including a -d custom mode.
• Updated unit tests and CLI documentation to cover the new behavior.

Reviewed changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated 1 comment.

File	Description
gff3tool/bin/gff3_to_fasta.py	Adds defline_attributes support, formatting helpers, CLI flag, and wiring through extraction/splicing paths.
tests/unit/test_gff3_to_fasta_cli.py	Updates call expectations for new parameter and adds a test for -d custom attribute-based deflines.
docs/gff3_to_fasta.md	Documents the new -da option and the custom defline mode.

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[codecov]

Codecov Report

❌ Patch coverage is 71.08434% with 24 lines in your changes missing coverage. Please review.
✅ Project coverage is 56.24%. Comparing base (e2e6bbd) to head (ea8ff0b).

Files with missing lines	Patch %	Lines
gff3tool/bin/gff3_to_fasta.py	71.08%	24 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #147      +/-   ##
==========================================
+ Coverage   54.86%   56.24%   +1.38%     
==========================================
  Files          28       28              
  Lines        5313     5378      +65     
==========================================
+ Hits         2915     3025     +110     
+ Misses       2398     2353      -45     

Files with missing lines	Coverage Δ
gff3tool/bin/gff3_to_fasta.py	56.00% <71.08%> (+12.58%)	⬆️

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[Copilot]

Pull request overview

Copilot reviewed 2 out of 3 changed files in this pull request and generated no new comments.

[ChrisChilders-USDA]

This looks ok to me