#!/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
import collections
from pypath.share import curl
from pypath.resources.urls import urls
CTD_URLS = {
'chemical_gene': 'CTD_chem_gene_ixns.tsv.gz',
'chemical_disease': 'CTD_chemicals_diseases.tsv.gz',
'disease_pathway': 'CTD_diseases_pathways.tsv.gz',
'chemical_phenotype': 'CTD_pheno_term_ixns.tsv.gz',
'gene_disease': 'CTD_genes_diseases.tsv.gz',
'chemical_vocabulary': 'CTD_chemicals.tsv.gz',
'gene_vocabulary': 'CTD_genes.tsv.gz',
'disease_vocabulary': 'CTD_diseases.tsv.gz',
'pathway_vocabulary': 'CTD_pathways.tsv.gz',
'anatomy_vocabulary': 'CTD_anatomy.tsv.gz',
'phenotype_vocabulary': 'CTD_phenotypes.tsv.gz',
}
def _ctdbase_download(_type: str) -> list[tuple]:
"""
Retrieves a CTDbase file and returns entries as a list of tuples.
"""
if '_' not in _type:
_type = f'{_type}_vocabulary'
url = urls['ctdbase']['url'] % CTD_URLS[_type]
c = curl.Curl(
url,
silent=False,
large=True,
encoding="utf-8",
default_mode="r",
compressed=True,
compr="gz",
)
entries = list()
fieldnames = None
for line in c.result:
if line.startswith("#"):
line = line.strip(" #\n").split("\t")
if len(line) > 1:
fieldnames = [fieldname for fieldname in line if fieldname != '']
record = collections.namedtuple('CTDEntry', fieldnames)
continue
data = line.split("\t")
# if data[-1] == "\n":
# del data[-1]
for i, v in enumerate(data):
is_list = "|" in v
has_sublist = "^" in v
if is_list:
v = v.split("|")
if has_sublist:
v = [element.split("^") for element in v]
elif has_sublist:
v = [v.split("^")]
data[i] = v
if len(data) != len(fieldnames):
continue # some lines have missing fields and cannot be parsed
entry = {}
for (fieldname, element) in zip(fieldnames, data):
if element == "":
element = None
else:
if type(element) == str:
element = element.strip()
elif type(element) == list:
element = [e.strip() if type(e) == str else e for e in element]
entry[fieldname] = element
if _type == 'chemical_phenotype':
entry = _modify_dict(entry,
('comentionedterms', ['name', 'id', 'source']),
('anatomyterms',['sequenceorder', 'name', 'id']),
('inferencegenesymbols',['name', 'id']),
('interactionactions',['interaction', 'action']),
)
if _type == 'gene_disease':
if entry['DirectEvidence'] == None:
continue
entries.append(record(**entry))
return entries
[docs]
def ctdbase_relations(relation_type: str) -> list[tuple]:
"""
Retrieves a CTDbase relation file.
For "gene-disease" relation type only curated relations are returned
(i.e. those with a "DirectEvidence" field) as the number of non-curated
relations is too large.
Args:
relation_type: One of the following:
'chemical_gene',
'chemical_disease',
'disease_pathway',
'chemical_phenotype',
'gene_disease',
Returns:
Relations as a list of tuples.
"""
return _ctdbase_download(relation_type)
[docs]
def ctdbase_vocabulary(vocabulary_type: str) -> list[tuple]:
"""
Retrieves a CTDbase vocabulary file.
Args:
vocabulary_type: One of the following:
'chemical',
'gene',
'disease',
'pathway',
'anatomy',
'phenotype',
Returns:
Vocabulary as a list of tuples.
"""
return _ctdbase_download(vocabulary_type)
def _modify_dict(_dict, *entry_pairs):
for key, new_keys in entry_pairs:
_dict[key] = _map_keys(
new_keys,
_dict[key]
)
return _dict
def _map_keys(keys, entry):
if entry == None:
return None
result = list()
for values in entry:
temp_dict = dict()
for key, value in zip(keys, values):
temp_dict[key] = value
result.append(temp_dict)
return result
