Protviz: Protein Annotation Visualiser

Protviz is a Python package designed to retrieve and visualise various protein annotations and structural information. It allows users to fetch data from multiple bioinformatics databases and plot this information along a protein sequence using a flexible track-based system.

Motivation

The goal of Protviz is to simplify the process of plotting protein annotations. This package is inspired by the Gviz library in R/Bioconductor, aiming to provide a similar, easy-to-use, track-based visualisation system for protein sequence data in Python.

I also wanted a way to plot data from resources but also be able to add custom annotations. Hope its helpful.

Features

• Data Retrieval:

  • Fetch protein sequence length from UniProt.
  • Retrieve PDB coverage and ligand interaction data from PDBe.
  • Get TED domain annotations from the TED database.
  • Fetch pLDDT scores and AlphaMissense data from the AlphaFold Database (AFDB).

• Track-Based Visualisation:

  • AxisTrack: Displays the sequence axis with tick marks.
  • PDBTrack: Shows PDB structure coverage, with options to display as individual entries or a collapsed overview.
  • LigandInteractionTrack: Visualises ligand binding sites on the protein from PDB.
  • TEDDomainsTrack: Displays TED annotations.
  • AlphaFoldTrack: Shows AlphaFold prediction metrics like pLDDT and average AlphaMissense pathogenicity scores.
  • CustomTrack: Allows plotting of arbitrary user-defined annotations (ranges or points) with customisable labels and colors.
  • InterProTrack: Displays InterPro annotations, like Pfam and CATH.

• Core Plotting Functionality:

  • Combines multiple tracks into a single, coherent plot.
  • Supports zooming into specific regions of the protein sequence.
  • Option to save plots to a file.

Dependencies

The package requires the following Python libraries:

• numpy>=1.20
• matplotlib>=3.4
• requests>=2.20
• gemmi (for parsing CIF files from AlphaFold DB)

Basic Usage

Here's a simple example of how to use Protviz to fetch data and plot tracks for a protein:

from protviz import plot_protein_tracks
from protviz.data_retrieval import get_protein_sequence_length, PDBeClient, AFDBClient
from protviz.tracks import AxisTrack, PDBTrack, AlphaFoldTrack

def main():
    uniprot_id = "O15245"  # Example UniProt ID

    # Initialize clients
    pdbe_client = PDBeClient()
    afdb_client = AFDBClient()

    try:
        # Fetch sequence length
        seq_length = get_protein_sequence_length(uniprot_id)
        print(f"Sequence length for {uniprot_id}: {seq_length}")

        # Fetch PDB coverage data
        pdb_coverage = pdbe_client.get_pdb_coverage(uniprot_id)
        print(f"Found {len(pdb_coverage)} PDB coverage entries.")

        # Fetch AlphaFold data (pLDDT)
        alphafold_data = afdb_client.get_alphafold_data(
            uniprot_id,
            requested_data_types=["plddt"]
        )
        print(f"Fetched AlphaFold data. pLDDT entries: {len(alphafold_data.get('plddt', []))}")

        # Create tracks
        axis_track = AxisTrack(sequence_length=seq_length, label="Sequence")

        pdb_track_collapsed = PDBTrack(
            pdb_data=pdb_coverage,
            label="PDB (Collapsed)",
            plotting_option="collapse",
            bar_height=0.1,
            color="darkturquoise"
        )

        alphafold_track_plddt = AlphaFoldTrack(
            afdb_data=alphafold_data,
            plotting_options=["plddt"],
            main_label="AF pLDDT",
            sub_track_height=0.2
        )

        # Plot the tracks
        plot_protein_tracks(
            protein_id=uniprot_id,
            sequence_length=seq_length,
            tracks=[axis_track, pdb_track_collapsed, alphafold_track_plddt],
            figure_width=12,
            save_option=True # Saves the plot as <uniprot_id>_plot.png
        )

        print(f"Plot saved as {uniprot_id}_plot.png")

    except Exception as e:
        print(f"An error occurred: {e}")
        import traceback
        traceback.print_exc()

if __name__ == "__main__":
    main()

Running Examples

The package includes several example scripts (e.g., example_pdbe.py, example_afdb.py, example_ted.py, example_pdbe_zoom.py) in the root directory or an examples/ folder.

To run an example, navigate to the directory containing the scripts and execute it with Python:

python examples/example_afdb.py