Source code for pybel.struct.mutation.inference.protein_rna_origins

# -*- coding: utf-8 -*-

"""Functions for enriching the origins of Proteins, RNAs, and miRNAs."""

from ...graph import BELGraph
from ...pipeline import in_place_transformation
from ....constants import FUNCTION, FUSION, MIRNA, RNA, VARIANTS
from ....dsl import Protein

__all__ = [

[docs]@in_place_transformation def enrich_proteins_with_rnas(graph: BELGraph) -> None: """Add the corresponding RNA node for each protein node and connect them with a translation edge. :param graph: A BEL graph """ for protein_node in list(graph): if not isinstance(protein_node, Protein): continue if protein_node.variants: continue rna_node = protein_node.get_rna() graph.add_translation(rna_node, protein_node)
[docs]@in_place_transformation def enrich_rnas_with_genes(graph: BELGraph) -> None: """Add the corresponding gene node for each RNA/miRNA node and connect them with a transcription edge. :param graph: A BEL graph """ for rna_node in list(graph): if rna_node[FUNCTION] not in {MIRNA, RNA} or FUSION in rna_node or VARIANTS in rna_node: continue gene_node = rna_node.get_gene() graph.add_transcription(gene_node, rna_node)
[docs]@in_place_transformation def enrich_protein_and_rna_origins(graph: BELGraph) -> None: """Add the corresponding RNA for each protein then the corresponding gene for each RNA/miRNA. :param graph: A BEL graph """ enrich_proteins_with_rnas(graph) enrich_rnas_with_genes(graph)