#!/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 os
import sys
import textwrap
import collections
import bs4
import pypath.resources.urls as urls
import pypath.share.curl as curl
import pypath.share.common as common
import pypath.share.session as session
_logger = session.Logger(name = 'unichem_input')
_log = _logger._log
[docs]
def unichem_info():
"""
List of ID types in UniChem. See more details at
https://www.ebi.ac.uk/unichem/ucquery/listSources.
Returns
(list): A list of named tuples, each representing information about
one UniChem resource.
"""
UnichemSource = collections.namedtuple(
'UnichemSource',
(
'number',
'label',
'name',
'description',
'acquisition',
),
)
url = urls.urls['unichem']['sources']
c = curl.Curl(url, large = False, silent = False)
soup = bs4.BeautifulSoup(c.result, 'html.parser')
result = []
for table in soup.find_all('table'):
if table.find('tr').text.strip().startswith('src_id'):
for row in table.find_all('tr')[2:]:
fields = row.find_all('td')
result.append(
UnichemSource(
*(
field.text.strip()
for field in fields
)
)
)
return result
[docs]
def unichem_sources():
"""
ID type numeric codes and labels in UniChem. For more information see
`unichem_info`.
Returns
(dict): A dict with ID type numeric IDs as keys and ID type labels
as values.
"""
return dict(
(
s.number,
s.label,
)
for s in unichem_info()
)
[docs]
def unichem_mapping(id_type_a, id_type_b):
"""
Identifier translation data from UniChem.
Args
id_type_a (int,str): An ID type in UniChem: either the integer ID or
the string label of a resource. For a full list see
`unichem_sources`.
id_type_b (int,str): An ID type in UniChem, same way as
`id_type_a`.
Returns
(dict): A dictionary with ID translation data, keys are IDs of
`id_type_a`, values are sets of IDs of `id_type_b`.
"""
return (
_unichem_mapping(id_type_a, id_type_b) or
common.swap_dict(_unichem_mapping(id_type_b, id_type_a))
)
def _unichem_mapping(id_type_a, id_type_b):
"""
Identifier translation data from UniChem.
Args
id_type_a (int,str): An ID type in UniChem: either the integer ID or
the string label of a resource. For a full list see
`unichem_sources`.
id_type_b (int,str): An ID type in UniChem, same way as
`id_type_a`.
Returns
(dict): A dictionary with ID translation data, keys are IDs of
`id_type_a`, values are sets of IDs of `id_type_b`.
"""
src_to_label = unichem_sources()
label_to_src = common.swap_dict(src_to_label)
def get_src_id(id_type):
id_type = str(id_type)
_id_type = label_to_src.get(id_type, id_type)
if not _id_type.isdigit() or _id_type not in src_to_label:
msg = 'No such ID type: `%s`.' % id_type
_log(msg)
raise ValueError(msg)
return _id_type
id_type_a = get_src_id(id_type_a)
id_type_b = get_src_id(id_type_b)
url = urls.urls['unichem']['mapping'] % (id_type_a, id_type_a, id_type_b)
c = curl.Curl(
url,
large = True,
silent = False,
slow = True,
http2 = False,
)
if c.status == 404:
return {}
result = collections.defaultdict(set)
_ = next(c.result)
for r in c.result:
src_id, tgt_id = r.strip().split('\t')
result[src_id].add(tgt_id)
return dict(result)
[docs]
def info(source):
"""
Print information about one source.
Args
source (int,str): The numeric or string ID of one source.
"""
source = str(source)
for s in unichem_info():
if source in s[:3]:
info = [
'%s [number=%s, label=%s]' % (
s.name, s.number, s.label,
),
'',
'Description:',
]
info.extend(textwrap.wrap(s.description))
info.extend(['', 'Data acquisition:'])
info.extend(textwrap.wrap(s.acquisition))
info.append('')
sys.stdout.write(os.linesep.join(info))
sys.stdout.flush()
break
