feat: add rewrite_fasta tool

[ameynert]

Summary

• Ports rewrite_fasta.py from human-diversity-reference/scripts as a defopt-compatible toolkit tool
• Filters a FASTA file to retain only canonical chromosomes (chr1–22, X, Y, MT)
• Fixes a potential UnboundLocalError in the original by initialising keep=False before the loop
• Removes the unused header_line variable from the original

Test plan

• uv run --directory divref poe check-all passes

🤖 Generated with Claude Code

Summary by CodeRabbit

• New Features

  • Added FASTA filtering tool to retain only canonical chromosome contigs (chr1–chr22, chrX, chrY, chrMT) while removing non-canonical sequences.

• Tests

  • Added comprehensive test coverage for FASTA filtering functionality.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: f97523b4-6a4c-4a4a-8c88-069f4d0b9731

📥 Commits

Reviewing files that changed from the base of the PR and between df39e5e and d07c2c6.

📒 Files selected for processing (3)

• .gitignore
• divref/divref/tools/rewrite_fasta.py
• divref/tests/tools/test_rewrite_fasta.py

✅ Files skipped from review due to trivial changes (3)

• .gitignore
• divref/divref/tools/rewrite_fasta.py
• divref/tests/tools/test_rewrite_fasta.py

---

📝 Walkthrough

Walkthrough

Updated .gitignore to narrow the ignore pattern from **/claude to **/.claude. Added a new rewrite_fasta() tool that filters FASTA files to retain only canonical chromosome contigs (chr1–chr22, chrX, chrY, chrMT), with comprehensive test coverage.

Changes

Cohort / File(s)	Summary
Configuration .gitignore	Narrowed ignore pattern to target .claude (dot-prefixed) instead of claude entries.
FASTA Filtering Tool divref/divref/tools/rewrite_fasta.py	New module implementing rewrite_fasta() function that streams input FASTA line-by-line, builds canonical contig set, and writes only headers and sequences matching canonical chromosome names to output.
Tool Tests divref/tests/tools/test_rewrite_fasta.py	Comprehensive test suite validating FASTA filtering behavior: canonical contig retention, non-canonical contig filtering, mixed input handling, empty input, and multiline sequence preservation.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐰 With whiskers twitching, I filtered the DNA,
Keeping chromosomes canonical, tossing the gray,
Twenty-three keepers (plus X, Y, and MT divine),
Tests passed with a hop—the FASTA now shines! 🧬✨

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 34.78% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'feat: add rewrite_fasta tool' accurately describes the main change: introducing a new rewrite_fasta tool module with accompanying tests.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch am_04_rewrite_fasta

---

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (2)

divref/tests/conftest.py (1)

24-26: Consider adding a brief docstring for the datadir fixture.

Per coding guidelines, public functions/fixtures benefit from docstrings explaining their purpose.

📝 Proposed docstring

 `@pytest.fixture`
 def datadir() -> Path:
+    """Return the path to the test data directory."""
     return Path(__file__).parent / "data"

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@divref/tests/conftest.py` around lines 24 - 26, Add a brief docstring to the
datadir pytest fixture that describes its purpose and return value: explain that
datadir returns a pathlib.Path pointing to the tests "data" directory adjacent
to conftest.py so tests can load test data files; place the docstring
immediately below the def datadir(...) signature.

divref/tests/tools/test_rewrite_fasta.py (1)

1-53: Consider adding an error-case test for missing input file.

Per coding guidelines, new public functions require "at least one happy-path test + one error case." The happy-path coverage is excellent, but there's no test verifying behavior when the input file doesn't exist (expected: FileNotFoundError).

🧪 Suggested error case test

def test_raises_on_missing_input(tmp_path: Path) -> None:
    with pytest.raises(FileNotFoundError):
        rewrite_fasta(fasta_path=tmp_path / "nonexistent.fa", output_path=tmp_path / "out.fa")

As per coding guidelines: "New public functions require at least one happy-path test + one error case."

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@divref/tests/tools/test_rewrite_fasta.py` around lines 1 - 53, Add an
error-case test that asserts rewrite_fasta raises FileNotFoundError when the
input FASTA is missing: create a new test function (e.g.,
test_raises_on_missing_input) that calls rewrite_fasta(fasta_path=tmp_path /
"nonexistent.fa", output_path=tmp_path / "out.fa") inside a
pytest.raises(FileNotFoundError) context using the existing tmp_path fixture;
reference the rewrite_fasta function to locate where behavior is expected to
raise.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@divref/divref/tools/rewrite_fasta.py`:
- Line 24: Change the bare index access on the line sentinel to guard against
empty lines: replace the condition using line[0] (in the loop that processes
FASTA lines) with a check that the line is non-empty before inspecting the first
character (e.g., use line and line[0] == ">" or use line.startswith(">")).
Update the FASTA-reading loop in rewrite_fasta.py where the variable line is
tested so blank lines are skipped safely and no IndexError can occur.

---

Nitpick comments:
In `@divref/tests/conftest.py`:
- Around line 24-26: Add a brief docstring to the datadir pytest fixture that
describes its purpose and return value: explain that datadir returns a
pathlib.Path pointing to the tests "data" directory adjacent to conftest.py so
tests can load test data files; place the docstring immediately below the def
datadir(...) signature.

In `@divref/tests/tools/test_rewrite_fasta.py`:
- Around line 1-53: Add an error-case test that asserts rewrite_fasta raises
FileNotFoundError when the input FASTA is missing: create a new test function
(e.g., test_raises_on_missing_input) that calls
rewrite_fasta(fasta_path=tmp_path / "nonexistent.fa", output_path=tmp_path /
"out.fa") inside a pytest.raises(FileNotFoundError) context using the existing
tmp_path fixture; reference the rewrite_fasta function to locate where behavior
is expected to raise.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: d5886734-3cee-4947-aa92-b18a1059d690

📥 Commits

Reviewing files that changed from the base of the PR and between 403ece8 and df39e5e.

📒 Files selected for processing (8)

• .gitignore
• divref/divref/haplotype.py
• divref/divref/tools/rewrite_fasta.py
• divref/tests/conftest.py
• divref/tests/data/test.fa
• divref/tests/data/test.fa.fai
• divref/tests/test_haplotype.py
• divref/tests/tools/test_rewrite_fasta.py

[coderabbitai]

⚠️ Potential issue | 🟡 Minor

Potential IndexError on empty lines in the FASTA file.

If the input FASTA contains blank lines (e.g., between contigs or trailing newlines), line[0] will raise an IndexError. While well-formed FASTA files typically don't have empty lines, defensive handling would improve robustness.

🛡️ Proposed fix

         for line in tqdm.tqdm(f):
+            if not line.strip():
+                continue
             if line[0] == ">":

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@divref/divref/tools/rewrite_fasta.py` at line 24, Change the bare index
access on the line sentinel to guard against empty lines: replace the condition
using line[0] (in the loop that processes FASTA lines) with a check that the
line is non-empty before inspecting the first character (e.g., use line and
line[0] == ">" or use line.startswith(">")). Update the FASTA-reading loop in
rewrite_fasta.py where the variable line is tested so blank lines are skipped
safely and no IndexError can occur.