Source code for pypath.inputs.sider

#!/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 __future__ import annotations

from typing import NamedTuple

import collections

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




class SiderSideeffect(NamedTuple):
    umls_concept_on_label: str
    umls_concept_in_meddra: str
    side_effect: str





class SiderSideeffetFrequency(NamedTuple):
    umls_concept_on_label: str
    umls_concept_in_meddra: str
    side_effect: str
    frequency: float





class SiderSideeffectMeddra(NamedTuple):
    cid: str
    meddra_id: str
    side_effect_name: str





class SiderDrug(NamedTuple):
    name: str
    atc: str





def sider_drug_names() -> dict[str, set[tuple]]:
    """
    Retrieves drug information from the SIDER database.

    Returns:
        Drug PubChem CID, name and ATC information as a list of named tuples.
    """


    result = collections.defaultdict(set)
    attrs = {}

    for attr in ('name', 'atc'):

        url = urls.urls['sider'][f'drug_{attr}s']
        c = curl.Curl(url, large = True, silent = False)
        attrs[attr] = collections.defaultdict(list)

        for line in c.result:

            cid, value = line.strip('\n').split('\t')
            attrs[attr][cid].append(value)

    for cid in set.union(*map(set, attrs.values())):

        for atc in attrs['atc'].get(cid, (None,)):

            result[cid].add(SiderDrug(
                name = attrs['name'].get(cid, (None,))[0],
                atc = atc,
            ))

    return dict(result)





def sider_side_effects(freq: bool = False) -> dict[str, set[tuple]]:
    """
    Retrieves side effect information from the SIDER database.

    Args:
        freq:
            Retrieve the dataset with frequency information. This is
            an independent dataset with lower coverage.

    Returns:
        Drug PubChem CID, UMLS concept ids both for label and MedDra
        and side effect name.
    """

    record = SiderSideeffetFrequency if freq else SiderSideeffect
    result = collections.defaultdict(set)
    url = urls.urls['sider']['meddra_%s' % ('freq' if freq else 'all')]
    c = curl.Curl(url, large = True, silent = False)

    # essential features' indices
    indices = (2, 8, 9, 4) if freq else (2, 4, 5)

    for line in c.result:

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

        if not line:

            continue

        result[line[0]].add(
            record(**{
                key: line[i] or None
                for key, i in zip(record._fields, indices)
            })
        )

    return dict(result)





def sider_side_effect_frequencies() -> list[tuple]:
    """
    Retrieves side effect information from the SIDER database.

    Returns:
        Drug CID, UMLS concept ids both for label and MedDRA,
        frequency information and side effect name.

    Attention! -> `sider_side_effects` function returns about 20k more rows
    than this dataset, but without frequency information.
    """

    return sider_side_effects(freq = True)





def sider_meddra_side_effects() -> list[tuple]:
    """
    Retrieves MedDRA side effect information from the SIDER database.

    Returns:
        A list of named tuples containing the following fields:
        - cid: Drug PubChem CID
        - meddra_id: MedDRA ID for the side effect
        - side_effect_name: Name of the side effect
    """


    url_meddra_tsv = urls.urls['sider']['meddra_tsv']

    c = curl.Curl(
        url_meddra_tsv,
        large = True,
        silent = False,
    )

    result = set()

    for line in c.result:

        if not line.strip():
            continue

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

        if line[1] == 'PT':

            result.add(
                SiderSideeffectMeddra(
                    cid = line[0],
                    meddra_id = line[2],
                    side_effect_name = line[3],
                )
            )

    return list(result)