New features

[sanjaysgk]

Summary by Sourcery

Enable customizable protein ID parsing and isoform extraction, improve runner input handling and logging, update plot titles, and bump the package version with new example data

New Features:

• Allow custom delimiter patterns in extract_protein_ids for flexible accession splitting
• Add extract_protein_isoforms to parse and return protein isoform identifiers from accession strings

Enhancements:

• Enhance runner to accept single protein strings, comma-separated lists, or file paths with detailed logging and error handling
• Standardize and clarify plot titles to include the target protein identifier

Chores:

• Bump package version to 1.1.1-dev
• Add example data files for JCI146771_Mouse_peptides dataset

[sourcery-ai]

Reviewer's Guide

This PR refactors protein ID extraction by parameterizing split patterns and adding isoform parsing, enhances the runner’s handling and logging of provided protein lists, updates the package version, and includes new sample data files for testing.

Class diagram for updated PeptideDataProcessor methods

classDiagram
    class PeptideDataProcessor {
        +remove_ptm(peptide: str) str
        +extract_protein_ids(accession_value: str, protein_pattern=None) List[str]
        +extract_protein_isoforms(accession_value: str, protein_pattern: str = r'[,:;|/\\s]+') List[str]
        +find_peptide_position(peptide: str, protein_sequence: str) Tuple[int, int]
    }

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Class diagram for run_pipeline function changes

classDiagram
    class run_pipeline {
        +run_pipeline(...)
        specific_proteins
    }
    run_pipeline --> PeptideDataProcessor : uses
    class PeptideDataProcessor

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File-Level Changes

Change	Details	Files
Refactor protein ID extraction with parameterized patterns and isoform support	Added optional protein_pattern parameter to extract_protein_ids with default fallback Replaced static split regex with compiled or provided pattern Introduced extract_protein_isoforms to parse and extract isoform suffixes using regex	ProtPeptigram/DataProcessor.py
Enhance runner’s protein_list parsing and logging	Added detailed console.log messages for provided protein_list inputs Supported single string, comma-separated lists, and file-based inputs under a unified branch Wrapped file reading in try/except to handle missing files gracefully Updated visualization title format to include target protein	ProtPeptigram/runner.py
Bump package version	Updated version from "1.1.0-dev" to "1.1.1-dev"	ProtPeptigram/__init__.py
Include sample data and test output files	Added new CSV data files under data/ and example/data/ for demo purposes Included processed_peptides_prot-peptigram.csv in test_output for validation	data/JCI146771_Mouse_peptides_peaks_online copy.csv example/data/JCI146771_Mouse_peptides_peaks_online_Nopeptides_ingroups.csv test_output/processed_peptides_prot-peptigram.csv

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