Add curated PHROG marker counts

[linsalrob]

What changed

• require and validate the authoritative PHROG v4 annotation TSV (gzip or plain text)
• add curated, auditable read-level marker assignments and union categories
• emit raw, per-million-all-top-hit, and per-million-PHROG-hit marker matrices
• add observed-PHROG mapping and per-sample denominator/QC tables
• generate documentation that explains marker definitions and interpretation limits
• make the Pawsey counting job validate the database and publish atomically compressed results
• add focused synthetic regression tests for denominators, overlaps, exclusions, zero-hit samples, and malformed databases

Why

The existing workflow summarized PHROG IDs, annotations, and categories but did not provide conservative biological marker summaries. These additions make read-level marker abundance directly available while avoiding claims of definitive phage lifestyle classification.

Validation

• PYTHONDONTWRITEBYTECODE=1 python -m unittest discover -s tests -v — 3 tests passed
• bash -n pawsey_shortread/count_phrog_functions.slurm pawsey_shortread/mmseqs_add_phrog_function.slurm
• parsed the supplied real phrog_annot_v4.tsv.gz: 109,404 records, with marker matches in every implemented biological class
• git diff --cached --check

[Copilot]

Pull request overview

This PR extends the PHROG-counting workflow to require an authoritative PHROG v4 annotation TSV and to generate curated, auditable read-level biological marker count matrices (raw and per-million normalisations), along with supporting QC/denominator outputs and focused regression tests.

Changes:

• Added curated PHROG marker classification rules and emitted *_marker_{raw,norm_all,norm_phrog}.tsv plus mapping/QC summary tables.
• Required and validated an authoritative PHROG annotation TSV (plain or gz) and validated MMseqs report PHROG records against it.
• Updated the Pawsey SLURM job to validate the database and publish compressed outputs via a temporary directory; added synthetic unit tests covering key marker/denominator behaviors.

Reviewed changes

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

File	Description
bin/count_phrog_functions.py	Adds authoritative PHROG DB validation, marker classification/matrices, and mapping/QC outputs.
pawsey_shortread/count_phrog_functions.slurm	Validates PHROG DB presence/gzip integrity and publishes compressed results atomically via a temp dir.
tests/test_count_phrog_functions.py	Adds regression tests for marker counting, normalisation denominators, exclusions/overlaps, zero-hit samples, and malformed DB handling.

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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.

[linsalrob]

@codex please review

[chatgpt-codex-connector]

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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.