#!/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/
#
"""
Variant data from the Clinvar database.
"""
from __future__ import annotations
import io
import csv
import ctypes
import collections
import pypath.share.curl as curl
import pypath.resources.urls as urls
csv.field_size_limit(int(ctypes.c_ulong(-1).value // 2))
[docs]
def clinvar_raw() -> list[tuple]:
"""
Retrieves variant data from the Clinvar database.
Returns:
Variants as a list of named tuples.
"""
Variant = collections.namedtuple(
'Variant',
[
'allele',
'type',
'variant',
'entrez',
'genesymbol',
'clinical_significance',
'review_status',
'rs',
'phenotype_ids',
'phenotypes',
'otherids',
'origin',
'variation_id',
'assembly',
'chromosome',
'chromosome_accession',
],
defaults = None
)
url = urls.urls['clinvar']['url']
c = curl.Curl(url, large = True, silent = False)
c.gzfile.seek(1) # get rid of a stray `#` character
response = csv.DictReader(
io.TextIOWrapper(c.gzfile),
dialect = 'excel-tab',
)
result = set()
for row in response:
phenotype_ids = tuple(row['PhenotypeIDS'].replace('|', ';').replace(',', ';').split(';'))
phenotypes = tuple(row['PhenotypeList'].replace('|', ';').replace(',', ';').split(';'))
otherids = tuple(row['OtherIDs'].replace('|', ';').replace(',', ';').split(';'))
variant = Variant(
allele = row['AlleleID'],
type = row['Type'],
variant = row['Name'],
entrez = row['GeneID'],
genesymbol = row['GeneSymbol'],
clinical_significance = row['ClinicalSignificance'],
review_status = row['ReviewStatus'],
rs = row['RS# (dbSNP)'],
phenotype_ids = phenotype_ids,
phenotypes = phenotypes,
otherids = None if otherids[0] == '-' else otherids,
origin = row['OriginSimple'],
variation_id = row['VariationID'],
assembly = row['Assembly'],
chromosome = row['Chromosome'],
chromosome_accession = row['ChromosomeAccession'],
)
result.add(variant)
return list(result)
[docs]
def clinvar_citations() -> list[tuple]:
"""
Retrieves citation information of variants
Returns:
Citations as a list of named tuples.
"""
Citation = collections.namedtuple(
'Citation',
[
'allele',
'variation_id',
'nsv',
'citation_source',
'citation_id'
],
defaults=None
)
url = urls.urls['clinvar']['url_citations']
c = curl.Curl(url, large = True, silent = False)
response = csv.DictReader(
c.result,
delimiter = '\t',
)
result = set()
for row in response:
citation = Citation(
allele = row['#AlleleID'],
variation_id = row['VariationID'],
nsv = row['nsv'],
citation_source = row['citation_source'],
citation_id = row['citation_id']
)
result.add(citation)
return list(result)
