Czhu update novel orf

[zhuchcn]

Description

The Novel ORF peptide fasta header now follow the same format as the circRNA peptides.

Example:

ENST0004|ORF-45:132|SE-2100|2

Closes #...

Checklist

• This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
• This PR does NOT contain molecular files, compressed files, output files such as images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
• I have read the code review guidelines and the code review best practice on GitHub check-list.
• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
• I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.
• All test cases passed locally.

[Copilot]

Pull request overview

This PR standardizes novel-ORF peptide FASTA headers to use coordinate-style ORF IDs and a canonical token order consistent with circRNA peptide headers, updating both generation and parsing paths plus associated tests/docs.

Changes:

• Generate non-circ ORF IDs in ORF-START:END form (when transcript sequence is available) and serialize ORF tokens before variant tokens.
• Keep backward-compatible parsing for prior token orders while normalizing __str__ output to the canonical order.
• Update unit tests, documentation, and test fixture FASTA/table files to match the new header conventions.

Reviewed changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
moPepGen/svgraph/PeptideVariantGraph.py	Adds linear stop-codon caching + linear ORF stop inference and emits coordinate-style ORF IDs; updates circ no-stop readthrough behavior.
moPepGen/aa/VariantPeptideIdentifier.py	Updates parsing examples and normalizes serialization order (ORF before variants); improves gene token inference for novel-ORF-only headers.
moPepGen/pipeline/call_variant_workers.py	Passes tx_seq and codon_table into peptide calling so linear ORF IDs can be computed.
moPepGen/pipeline/call_novel_orf_worker.py	Passes tx_seq and codon_table into peptide calling for novel ORF workflows.
test/unit/test_peptide_variant_graph.py	Adds/updates tests for linear ORF coordinate IDs and circRNA no-stop sentinel behavior.
test/unit/test_variant_peptide_id.py	Adds parsing/roundtrip tests for canonical ORF-before-variant ordering and legacy order compatibility.
test/unit/test_peptide_pool_summarizer.py	Updates expected header ordering and adds coverage for novel ORF coordinate headers.
test/unit/test_peptide_pool_splitter.py	Updates expected header ordering and adds split coverage for novel ORF coordinate headers and mixed-label inputs.
docs/file-format.md	Documents the non-circ novel ORF header style and coordinate ORF ID notation.
test/files/peptides/variant_peptide_table.txt	Updates fixture content to align with new ORF/header conventions (ordering/IDs).
test/files/peptides/variant.fasta	Updates fixture FASTA headers/order to match new conventions.
test/files/peptides/novel_orf.fasta	Updates novel ORF fixture FASTA headers to coordinate-style ORF IDs and revised ordering.
test/files/peptides/alt_translation.fasta	Updates fixture FASTA to match revised header formatting/order.
CHANGELOG.md	Notes the novel-ORF header format changes and backward-compatible parsing behavior.

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