Source code for pypath.inputs.transmir

#!/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 bs4

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



[docs] def transmir_interactions(): """ TF-miRNA gene intractions from TransmiR. """ url = urls.urls['transmir']['url'] c = curl.Curl( url, silent = False, large = True, encoding = 'iso-8859-1', ) TransmirInteraction = collections.namedtuple( 'TransmirInteraction', [ 'tf_genesymbol', 'mirna', 'effect', 'pubmed', ] ) result = [] for l in c.result: l = l.strip().split('\t') result.append( TransmirInteraction( tf_genesymbol = l[0], mirna = l[1], effect = l[4].split('(')[0], pubmed = l[5], ) ) return result