Source code for graphein.ppi.features.node_features

"""Functions for adding nodes features to a PPI Graph"""
import logging

# %%
# Graphein
# Author: Ramon Vinas, Arian Jamasb <>
# License: MIT
# Project Website:
# Code Repository:
from typing import Any, Dict

import networkx as nx

from graphein.utils.utils import import_message

log = logging.getLogger(__name__)

    from bioservices import HGNC, UniProt
except ImportError:
    message = import_message(

[docs]def add_sequence_to_nodes(n: str, d: Dict[str, Any]): """ Maps UniProt ACC to UniProt ID. Retrieves sequence from UniProt and adds it to the node as a feature :param n: Graph node. :type n: str :param d: Graph attribute dictionary. :type d: Dict[str, Any] """ h = HGNC(verbose=False) u = UniProt(verbose=False) d["uniprot_ids"] = h.fetch("symbol", d["protein_id"])["response"]["docs"][ 0 ]["uniprot_ids"] # Todo these API calls should probably be batched # Todo mapping with bioservices to support other protein IDs? for id in d["uniprot_ids"]: d[f"sequence_{id}"] = u.get_fasta_sequence(id)
if __name__ == "__main__": from functools import partial import matplotlib.pyplot as plt from graphein.ppi.config import PPIGraphConfig from graphein.ppi.edges import add_biogrid_edges, add_string_edges from graphein.ppi.graphs import compute_ppi_graph protein_list = [ "CDC42", "CDK1", "KIF23", "PLK1", "RAC2", "RACGAP1", "RHOA", "RHOB", ] config = PPIGraphConfig() kwargs = config.kwargs g = compute_ppi_graph( protein_list=protein_list, edge_construction_funcs=[ partial(add_string_edges, kwargs=kwargs), partial(add_biogrid_edges, kwargs=kwargs), ], ) for n, d in g.nodes(data=True): add_sequence_to_nodes(n, d) print(nx.get_node_attributes(g, "sequence")) edge_colors = [ "r" if g[u][v]["kind"] == {"string"} else "b" if g[u][v]["kind"] == {"biogrid"} else "y" for u, v in g.edges() ] print( nx.draw(g, with_labels=True, edge_color=edge_colors)