#!/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 typing import List, Optional
from numbers import Number
import collections
import pypath.resources.urls as urls
import pypath.share.curl as curl
[docs]
def biogrid_interactions(
organism: int = 9606,
htp_limit: Optional[Number] = 1,
ltp: bool = True,
) -> List[tuple]:
"""
Downloads and processes Physical multi-validated BioGRID interactions.
Keeps only the "low throughput" interactions.
Returns list of interactions.
Args
organism: NCBI Taxonomy ID of organism.
htp_limit: Exclude interactions only from references cited at more
than this number of interactions.
"""
BiogridPhysicalInteraction = collections.namedtuple(
'BiogridPhysicalInteraction',
(
'partner_a',
'partner_b',
'pmid',
),
)
organism = str(organism)
interactions = []
refc = []
url = urls.urls['biogrid']['mv']
c = curl.Curl(url, silent = False, large = True, slow = True)
f = next(iter(c.result.values()))
nul = f.readline()
for l in f:
l = l.split('\t')
if len(l) > 17:
if (
(
l[17].startswith('Low') or
not ltp
) and (
organism == 'None' or (
l[15] == organism and
l[16] == organism
)
)
):
interactions.append(
BiogridPhysicalInteraction(
partner_a = l[7],
partner_b = l[8],
pmid = l[14],
)
)
refc.append(l[14])
refc = collections.Counter(refc)
if htp_limit is not None:
interactions = [i for i in interactions if refc[i[2]] <= htp_limit]
return interactions
[docs]
def biogrid_all_interactions(
organism: int = 9606,
htp_limit: Optional[Number] = 1,
ltp: bool = True,
) -> List[tuple]:
"""
Downloads and processes all BioGRID interactions.
Keeps only the "low throughput" interactions.
Returns list of interactions.
Args
organism: NCBI Taxonomy ID of organism.
htp_limit: Exclude interactions only from references cited at
more than this number of interactions.
"""
BiogridInteraction = collections.namedtuple(
'BiogridInteraction',
(
'partner_a',
'partner_b',
'pmid',
'experimental_system',
'experimental_system_type',
'ltp',
'htp_score',
'multi_validated',
'tax_a',
'tax_b',
),
)
organism = str(organism)
interactions = []
refc = []
mv_dict=collections.defaultdict(list)
for i in biogrid_interactions(organism, htp_limit, ltp):
mv_dict[i.partner_a].append(i.partner_b)
url = urls.urls['biogrid']['all']
c = curl.Curl(url, silent = False, large = True, slow = True)
f = next(iter(c.result.values()))
nul = f.readline()
for l in f:
l = l.split('\t')
if len(l) > 17:
if (
(
l[17].startswith('Low') or
not ltp
) and (
organism == 'None' or (
l[15] == organism and
l[16] == organism
)
)
):
mv = l[8] in mv_dict[l[7]] or l[7] in mv_dict[l[8]]
interactions.append(
BiogridInteraction(
partner_a = l[7],
partner_b = l[8],
pmid = l[14],
experimental_system = l[11],
experimental_system_type = l[12],
ltp = 'Low T' in l[17],
htp_score = None if l[18] == '-' else float(l[18]),
multi_validated = mv,
tax_a = l[15],
tax_b = l[16],
)
)
refc.append(l[14])
refc = collections.Counter(refc)
if htp_limit is not None:
interactions = [i for i in interactions if refc[i[2]] <= htp_limit]
return interactions
