Source code for pypath.inputs.intogen

#!/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 past.builtins import xrange, range

import csv
import collections

import pypath.resources.urls as urls
import pypath.share.curl as curl
import pypath.share.common as common
import pypath.share.settings as settings
import pypath.utils.mapping as mapping



[docs]
def intogen_annotations():
    """
    Returns a list of cancer driver genes with their annotations,
    according to the IntOGen database.
    """

    IntogenAnnotation = collections.namedtuple(
        'IntogenAnnotation',
        [
            'type',
            'role',
            'curated',
            'oncodrive_role_prob',
        ],
    )


    url = urls.urls['intogen']['db2014_2']

    with settings.context(curl_connect_timeout = 100):

        c = curl.Curl(
            url,
            large = True,
            silent = False,
            files_needed = ['Drivers_type_role.tsv'],
            compr = 'zip',
        )

    for _ in xrange(7):

        __ = c.result['Drivers_type_role.tsv'].readline()

    data = csv.DictReader(
        c.result['Drivers_type_role.tsv'],
        delimiter = '\t',
    )
    result = collections.defaultdict(set)

    for rec in data:

        uniprots = mapping.map_name(
            rec['geneHGNCsymbol'],
            'genesymbol',
            'uniprot',
        )

        for uniprot in uniprots:

            role_prob, curated = (
                (
                    1.0,
                    True,
                )
                if rec['OncodriveROLE_prob'] == 'Manually curated' else
                (
                    common.float_or_nan(rec['OncodriveROLE_prob']),
                    False,
                )
            )

            result[uniprot].add(
                IntogenAnnotation(
                    type = rec['Driver_type'],
                    role = rec['Role'],
                    curated = curated,
                    oncodrive_role_prob = role_prob,
                )
            )

    return dict(result)