updated new

[sanjaysgk]

Summary by Sourcery

Integrate a real-time progress bar into peptide filtering, refine isoform extraction regex, and streamline ImmunoViz integration.

Enhancements:

• Add a rich.Progress-based progress bar to the peptide-to-protein alignment loop in filter_and_format_data.
• Refine the regex in extract_protein_isoforms to correctly handle whitespace delimiters.
• Streamline the create_immunoviz_object method by updating the ImmunoViz type hint and removing a redundant import.

[sourcery-ai]

Reviewer's Guide

This PR enhances DataProcessor by adding a real-time progress bar for peptide-to-protein alignment, centralizing key imports at the module level, refining the isoform splitting regex, and simplifying the ImmunoViz object creation signature.

Sequence diagram for peptide-to-protein alignment with progress bar

sequenceDiagram
    participant DataProcessor
    participant ProgressBar as Progress
    participant DataFrame as data
    participant ProteinDB as get_protein_sequence
    participant Output as formatted_rows
    DataProcessor->>ProgressBar: Start progress bar (total = len(data))
    loop For each row in data
        DataProcessor->>DataFrame: Get peptide, accession, intensities
        DataProcessor->>DataProcessor: extract_protein_ids
        alt protein_ids found
            loop For each protein_id
                DataProcessor->>ProteinDB: get_protein_sequence(protein_id)
                alt sequence found
                    DataProcessor->>DataProcessor: find_peptide_position
                else sequence not found
                    DataProcessor->>DataProcessor: Use placeholder positions
                end
                DataProcessor->>Output: Append formatted row if intensity > threshold
            end
        end
        DataProcessor->>ProgressBar: Update progress
    end
    ProgressBar-->>DataProcessor: Complete

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Class diagram for updated PeptideDataProcessor structure

classDiagram
    class PeptideDataProcessor {
        +extract_protein_ids(accession_value: str, protein_pattern=None) List[str]
        +extract_protein_isoforms(accession_value: str, protein_pattern: str = r'[,:;|/\s]+') List[str]
        +filter_and_format_data(...)
        +get_protein_sequence(protein_id: str) Optional[str]
        +create_immunoviz_object() ImmunoViz
        -intensity_cols
        -sample_prefix
        -peptide_df
    }
    class ImmunoViz
    PeptideDataProcessor --> ImmunoViz : creates

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Class diagram for ImmunoViz import and type annotation update

classDiagram
    class PeptideDataProcessor {
        +create_immunoviz_object() ImmunoViz
    }
    class ImmunoViz
    PeptideDataProcessor --> ImmunoViz : returns

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File-Level Changes

Change	Details	Files
Integrate rich.Progress-based progress bar in filter_and_format_data	Wrap peptide-to-protein alignment loop in a Progress context Add and update a progress task for each peptide processed Advance progress after handling each peptide	ProtPeptigram/DataProcessor.py
Centralize module imports for Progress and ImmunoViz	Move import of ImmunoViz and rich.Progress to top of the module Remove redundant in-function import of ImmunoViz	ProtPeptigram/DataProcessor.py
Refine protein isoform splitting regex	Adjust default regex to correctly include whitespace as a delimiter	ProtPeptigram/DataProcessor.py
Simplify create_immunoviz_object signature and import logic	Change return type annotation to use ImmunoViz directly Eliminate circular-import workaround inside the function	ProtPeptigram/DataProcessor.py

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