#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This file is part of the `pypath` python module
#
# Copyright 2014-2023
# EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University
#
# Authors: see the file `README.rst`
# Contact: Dénes Türei (turei.denes@gmail.com)
#
# Distributed under the GPLv3 License.
# See accompanying file LICENSE.txt or copy at
# https://www.gnu.org/licenses/gpl-3.0.html
#
# Website: https://pypath.omnipathdb.org/
#
from future.utils import iteritems
import sys
import re
import collections
import itertools
import pypath.share.curl as curl
import pypath.resources.urls as urls
import pypath.share.common as common
import pypath.utils.mapping as mapping
[docs]
def signalink_interactions(organism = 9606, exclude_secondary = True):
"""
Reads and processes SignaLink3 interactions from local file.
Returns list of interactions.
"""
SignalinkInteraction = collections.namedtuple(
'SignalinkInteraction',
[
'id_a',
'id_b',
'is_direct',
'is_directed',
'effect',
'pathways_a',
'pathways_b',
'functions_a',
'functions_b',
'references',
'resources',
]
)
signalink_sources = {
'SLKv2.0',
'SLKv2.1',
'SLKv3.0',
'SignaFish',
'TCRcuration',
}
repref = re.compile(r'(?:.*:)?((?:[\w]+[^\s])?)\s?')
nodes_pathways = {}
nodes_organism = {}
nodes_functions = {}
interactions = []
def get_value(field):
return repref.sub('\\1', field)
def get_values(field):
return [get_value(f) for f in field.split('|')]
url_nodes = urls.urls['signalink']['nodes']
c_nodes = curl.Curl(url_nodes, silent = False, large = True)
url_edges = urls.urls['signalink']['edges']
c_edges = curl.Curl(url_edges, silent = False, large = True)
_ = next(c_nodes.result)
for l in c_nodes.result:
l = l.strip('\n\r')
if l:
l = l.split('\t')
_id = int(l[0])
uniprot = get_value(l[1])
pathways = (
l[4].replace('/Wingless', '').split('|') if l[4] else []
)
_organism = int(get_value(l[3]))
nodes_pathways[uniprot] = pathways
nodes_organism[uniprot] = _organism
nodes_functions[uniprot] = l[6].split('|') if l[6] else []
_ = next(c_edges.result)
for l in c_edges.result:
l = l.strip().split('\t')
if exclude_secondary and not set(l[6].split('|')) & signalink_sources:
continue
id_a = get_value(l[0])
id_b = get_value(l[1])
if (
nodes_organism[id_a] != organism or
nodes_organism[id_b] != organism
):
continue
resources = [
res for res in get_values(l[6])
if not res.startswith('SLK')
]
interaction_attrs = {
tuple(iattr.split(':'))
for iattr in l[5].split('|')
}
effects = []
if ('MI', '0624(stimulation)') in interaction_attrs:
effects.append(1)
if ('MI', '0623(inhibition)') in interaction_attrs:
effects.append(-1)
if not effects:
effects.append(0)
for effect in effects:
interactions.append(
SignalinkInteraction(
id_a = id_a,
id_b = id_b,
is_direct = ('is_direct', 'true') in interaction_attrs,
is_directed = ('is_directed', 'true') in interaction_attrs,
effect = effect,
pathways_a = nodes_pathways[id_a],
pathways_b = nodes_pathways[id_b],
functions_a = nodes_functions[id_a],
functions_b = nodes_functions[id_b],
references = get_values(l[4]),
resources = resources,
)
)
return interactions
[docs]
def signalink_annotations(organism = 9606):
SignalinkPathway = collections.namedtuple(
'SignalinkPathway',
[
'pathway',
]
)
SignalinkFunction = collections.namedtuple(
'SignalinkFunction',
[
'function',
]
)
result = {
'pathway': collections.defaultdict(set),
'function': collections.defaultdict(set),
}
interactions = signalink_interactions(organism = organism)
for i in interactions:
for postfix in ('_a', '_b'):
_id = getattr(i, 'id%s' % postfix)
for uniprot in mapping.map_name(_id, 'uniprot', 'uniprot'):
for attr, record in zip(
('pathway', 'function'),
(SignalinkPathway, SignalinkFunction),
):
values = getattr(i, '%ss%s' % (attr, postfix))
for value in values:
result[attr][uniprot].add(
record(value)
)
return dict((k, dict(v)) for k, v in iteritems(result))
[docs]
def signalink_pathway_annotations(organism = 9606):
return signalink_annotations(organism = organism)['pathway']
[docs]
def signalink_function_annotations(organism = 9606):
return signalink_annotations(organism = organism)['function']
