#!/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 numbers import Number
from typing import List
import collections
import pypath.resources.urls as urls
import pypath.share.curl as curl
import pypath.share.progress as progress
[docs]
def intact_interactions(
miscore: Number = .6,
organism: int = 9606,
complex_expansion: bool = False,
only_proteins: bool = False,
only_ids: bool = False,
) -> List[tuple]:
"""
only_proteins : bool
Keep only records of protein-protein interactions.
only_ids : bool
Load only the identifiers of interacting pairs
(smaller memory footprint).
"""
id_types = {
'uniprotkb': 'uniprot',
}
IntactInteraction = collections.namedtuple(
'IntactInteraction',
(
'id_a',
'id_b',
'id_type_a',
'id_type_b',
'pubmeds',
'methods',
'interaction_types',
'mi_score',
'isoform_a',
'isoform_b',
),
)
IntactInteraction.__new__.__defaults__ = (None,) * 7
def get_id_type(field):
id_type = None if field == '-' else field.split(':')[0]
return id_types[id_type] if id_type in id_types else id_type
def get_uniprot_id(field):
uniprot, isoform = _try_isoform(
field.split(':')[1].replace('"', '')
)
uniprot = uniprot.split('-')[0]
return uniprot, isoform
def get_ebi_id(field):
if field == '-':
return None, None
else:
partner_id=field.split(':')[1]
return partner_id, None
def get_taxon(field):
return (
0
if field == '-' else
field.split('|')[0].split(':')[1].split('(')[0]
)
results = []
url = urls.urls['intact']['mitab']
if type(organism) is int:
organism = '%u' % organism
c = curl.Curl(
url,
silent = False,
large = True,
files_needed = ['intact.txt'],
slow = True,
)
data = c.result['intact.txt']
size = c.sizes['intact.txt']
prg = progress.Progress(size, 'Reading IntAct MI-tab file', 99)
for lnum, l in enumerate(data):
prg.step(len(l))
if lnum == 0:
continue
l = l.strip('\n\r ').split('\t')
taxon_a = get_taxon(l[9])
taxon_b = get_taxon(l[10])
if (
(
organism is None or (
taxon_a == organism and
taxon_b == organism
)
) and (
complex_expansion or
'expansion' not in l[15]
)
):
# finding mi-score and author
sc = 0
au = '0'
for s in l[14].split('|'):
if s.startswith('intact-miscore'):
sc = float(s.split(':')[1])
if s.startswith('author'):
au = len(s.split(':')[1])
# filtering for mi-score
if sc < miscore:
continue
id_type_a = get_id_type(l[0])
id_type_b = get_id_type(l[1])
if (
only_proteins and not (
id_type_a == 'uniprot' and
id_type_b == 'uniprot'
)
):
continue
id_a, isoform_a = (
get_uniprot_id(l[0])
if id_type_a == 'uniprot' else
get_ebi_id(l[0])
)
id_b, isoform_b = (
get_uniprot_id(l[1])
if id_type_b == 'uniprot' else
get_ebi_id(l[1])
)
# key = tuple(sorted((id_a, id_b)))
pubmeds = set(
ref[1] for ref in (
ref.split(':')
for ref in l[8].split('|')
)
if ref[0] == 'pubmed'
)
methods = set(
met.split('(')[1].strip(')"')
for met in l[6].split('|')
)
interaction_types= set(
int_type.split('(')[1].strip(')"')
for int_type in l[11].split('|')
)
results.append(
IntactInteraction(
id_a = id_a,
id_b = id_b,
id_type_a = id_type_a,
id_type_b = id_type_b,
pubmeds = pubmeds,
methods = methods,
interaction_types = interaction_types,
mi_score = sc,
isoform_a = isoform_a,
isoform_b = isoform_b,
)
)
prg.terminate()
return results
def _try_isoform(name):
name = name.split('-')
if len(name) > 1 and name[1].isdigit():
isoform = int(name[1])
main = name[0]
else:
main = '-'.join(name)
isoform = None
return main, isoform
