Source code for pypath.inputs.ca1

#!/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 collections

import pypath.resources.urls as urls
import pypath.share.curl as curl
import pypath.inputs.science as science_input



[docs]
def ca1_interactions():
    """
    Downloads and processes the CA1 signaling network (Ma\'ayan 2005).
    Returns list of interactions.
    """

    Ca1Interaction = collections.namedtuple(
        'Ca1Interaction',
        (
            'genesymbol_source',
            'uniprot_source',
            'uniprot_mouse_source',
            'function_source',
            'location_source',
            'genesymbol_target',
            'uniprot_target',
            'uniprot_mouse_target',
            'function_target',
            'location_target',
            'effect',
            'interaction_type',
            'pmid',
        ),
    )

    url = urls.urls['ca1']['url']
    path = science_input.science_download(url = url)
    zipfile = curl.FileOpener(
        path,
        compr = 'zip',
        files_needed = ['S1.txt'],
        large = False,
    )
    data = zipfile.result
    result = []

    for l in data['S1.txt'].decode('ascii').split('\n')[1:]:

        l = l.strip().split()

        if len(l) == 13:

            result.append(Ca1Interaction(*l))

    return result