Add Mode to splitFasta to Split Peptides by FASTA Entry

[zhuchcn]

Description

Add --split-mode to splitFasta with two modes:

• peptide (default): existing behavior, one tier per peptide sequence
• entry: split by individual FASTA header entry, so shared peptides can appear in multiple tiers

Closes #17

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 adds a --split-mode option to the splitFasta command, enabling two split behaviors: the existing peptide mode (one FASTA record per unique peptide sequence assigned to a single tier) and a new entry mode (each individual FASTA header entry is routed to its own tier, allowing the same peptide sequence to appear in multiple tier files under different labels).

Changes:

• PeptidePoolSplitter.split() gains a split_mode parameter; the existing assignment logic is extracted into add_peptide_to_database_peptide_mode(), a new add_peptide_to_database_entry_mode() handles per-entry routing, and shared key-resolution is factored into get_database_key().
• The splitFasta CLI argument parser gains a --split-mode argument (choices: peptide, entry), and its handler passes the value to the splitter.
• Unit and integration tests are added for both modes, and documentation is updated.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
moPepGen/aa/PeptidePoolSplitter.py	Adds split_mode parameter, extracts per-mode methods, adds validation
moPepGen/cli/split_fasta.py	Adds --split-mode CLI argument and passes it to splitter.split()
test/unit/test_peptide_pool_splitter.py	Adds unit tests for entry and peptide mode split behavior
test/integration/test_split_fasta.py	Adds base args default and integration test for entry mode
docs/split-fasta.md	Documents the new --split-mode option
CHANGELOG.md	Records the new feature under the unreleased section

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.