#!/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 Generator, Literal
import collections
import pandas as pd
import pypath.share.curl as curl
import pypath.resources.urls as urls
_molecule_fields =(
'pathway_id',
'url',
'pathway_name',
'evidence_code',
'organism'
)
_FIELDS = {
'uniprot2all': ('uniprot_id',) + _molecule_fields,
'chebi2all': ('chebi_id',) + _molecule_fields,
'pathways': (
'pathway_id',
'pathway_name',
'organism',
),
'pathway_relations': (
'parent',
'child',
),
}
_RECORD_NAMES = {
'uniprot2all': 'Uniprot',
'chebi2all': 'Chebi',
'pathways': 'Pathway',
'pathway_relations': 'PathwayRelation',
}
def _reactome_data(
dataset: Literal[
'uniprot2all',
'chebi2all',
'pathways',
'pathway_relations',
],
return_df: bool = False,
) -> Generator[tuple] | pd.DataFrame:
"""
Retrieves pathway information by given input
Args:
source:
- uniprot2all (fields: uniprot_id, pathway_id, url,
pathway_name, evidence_code, organism)
- chebi2all (fields: chebi_id, pathway_id, url,
pathway_name, evidence_code, organism)
- pathways (fields: pathway_id, pathway_name, organism)
- pathway_relations (fields: parent, child)
return_df:
Return a pandas data frame.
Returns:
Records of the requested dataset.
"""
result = _reactome_data_gen(dataset)
return pd.DataFrame(result) if return_df else result
def _reactome_data_gen(
dataset: Literal[
'uniprot2all',
'chebi2all',
'pathways',
'pathway_relations',
]
) -> Generator[tuple]:
url = urls.urls['reactome'][dataset]
c = curl.Curl(url, large = True)
result = set()
record = collections.namedtuple('Reactome', fields)
for line in c.result:
line = line.strip('\n').split('\t')
yield record(*line)
[docs]
def reactome_uniprots(
return_df: bool = False,
) -> Generator[tuple] | pd.DataFrame:
"""
UniProt mappings from Reactome.
Args:
return_df:
Return a pandas data frame.
"""
return _reactome_data('uniprot2all', return_df = return_df)
[docs]
def reactome_chebis(
return_df: bool = False,
) -> Generator[tuple] | pd.DataFrame:
"""
ChEBI mappings from Reactome.
Args:
return_df:
Return a pandas data frame.
"""
return _reactome_data('chebi2all', return_df = return_df)
[docs]
def reactome_pathways(
return_df: bool = False,
) -> Generator[tuple] | pd.DataFrame:
"""
The list of pathways in Reactome.
Args:
return_df:
Return a pandas data frame.
"""
return _reactome_data('pathways', return_df = return_df)
[docs]
def reactome_pathway_relations(
return_df: bool = False,
) -> Generator[tuple] | pd.DataFrame:
"""
The Reactome pathway hierarchy (ontology).
Args:
return_df:
Return a pandas data frame.
"""
return _reactome_data('pathway_relations', return_df = return_df)
