Source code for pypath.inputs.acsn

#!/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/
#

import re
import collections

import pypath.resources.urls as urls
import pypath.share.curl as curl



[docs]
def acsn_interactions(keep_in_complex_interactions = True):
    """
    Processes ACSN data from local file.
    Returns list of interactions.

    @keep_in_complex_interactions : bool
        Whether to include interactions from complex expansion.
    """

    AcsnInteraction = collections.namedtuple(
        'AcsnInteraction',
        (
            'partner_a',
            'partner_b',
            'mechanism',
            'references',
        ),
    )

    names_url = urls.urls['acsn']['names']
    ppi_url = urls.urls['acsn']['ppi']
    names_c = curl.Curl(names_url, silent = False, large = True)
    ppi_c = curl.Curl(ppi_url, silent = False, large = True)

    names = {}
    interactions = []

    for l in names_c.result:

        l = l.strip().split('\t')
        names[l[0]] = l[2:]

    _ = next(ppi_c.result)

    for l in ppi_c.result:

        l = l.strip().split('\t')

        if l[0] in names:

            for a in names[l[0]]:

                if l[2] in names:

                    for b in names[l[2]]:

                        if keep_in_complex_interactions:

                            if 'PROTEIN_INTERACTION' in l[1]:

                                l[1].replace(
                                    'COMPLEX_EXPANSION',
                                    'IN_COMPLEX_INTERACTION'
                                )

                        interactions.append(
                            AcsnInteraction(
                                partner_a = a,
                                partner_b = b,
                                mechanism = l[1],
                                references = l[3].replace('N/A', ''),
                            )
                        )

    return interactions




[docs]
def acsn_interactions_sif():
    """
    Retrieves the ACSN interactions by the SIF format distributed from the
    official website.
    """

    greek = {
        '_alpha_': 'A',
        '_beta_': 'B',
        '_gamma_': 'C',
        '_delta_': 'D',
        '_epsilon_': 'E'
    }
    regreek = re.compile(r'\b(' + '|'.join(greek.keys()) + r')\b')
    result = []
    url = urls.urls['acsn']['sif']
    c = curl.Curl(url, silent = False)
    data = c.result
    data = [
        x.split('\t')
        for x in data.replace('\r', '').replace('*', '').strip().split('\n')
    ]

    for l in data:
        l[0] = regreek.sub('', l[0]).split('_')[0].split('~')[0]
        l[2] = regreek.sub('', l[2]).split('_')[0].split('~')[0]

    return data