# -*- coding: utf-8 -*-
"""Functions for deleting proteins and genes that are leaves."""
from typing import Iterable
from ...filters.node_filters import get_nodes_by_function
from ...pipeline.decorators import in_place_transformation
from ....constants import GENE, RELATION, RNA, TRANSCRIBED_TO, TRANSLATED_TO
from ....dsl import BaseEntity
__all__ = [
'prune_protein_rna_origins',
]
def get_gene_leaves(graph) -> Iterable[BaseEntity]:
"""Iterate over all genes who have only one connection, that's a transcription to its RNA.
:param pybel.BELGraph graph: A BEL graph
"""
yield from _iterate_leaves(graph, GENE, TRANSCRIBED_TO)
def get_rna_leaves(graph) -> Iterable[BaseEntity]:
"""Iterate over all RNAs who have only one connection, that's a translation to its protein.
:param pybel.BELGraph graph: A BEL graph
"""
yield from _iterate_leaves(graph, RNA, TRANSLATED_TO)
def _iterate_leaves(graph, func, relation):
for node in get_nodes_by_function(graph, func):
if graph.in_degree(node) != 0:
continue
if graph.out_degree(node) != 1:
continue
_, _, d = list(graph.out_edges(node, data=True))[0]
if d[RELATION] == relation:
yield node
@in_place_transformation
def prune_rna_origins(graph):
"""Delete gene nodes that are only connected to one node, their correspond RNA, by a transcription edge.
:param pybel.BELGraph graph: A BEL graph
"""
gene_leaves = list(get_gene_leaves(graph))
graph.remove_nodes_from(gene_leaves)
@in_place_transformation
def prune_protein_origins(graph):
"""Delete RNA nodes that are only connected to one node - their correspond protein - by a translation edge.
:param pybel.BELGraph graph: A BEL graph
"""
rna_leaves = list(get_rna_leaves(graph))
graph.remove_nodes_from(rna_leaves)
[docs]@in_place_transformation
def prune_protein_rna_origins(graph):
"""Delete genes that are only connected to one node, their correspond RNA, by a translation edge.
:param pybel.BELGraph graph: A BEL graph
"""
prune_rna_origins(graph)
prune_protein_origins(graph)