#!/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 past.builtins import xrange, range
import re
import collections
import bs4
import pypath.share.curl as curl
import pypath.resources.urls as urls
[docs]
def elm_domains():
url = urls.urls['ielm_domains']['url']
c = curl.Curl(url, silent = False)
data = c.result
soup = bs4.BeautifulSoup(data, 'html.parser')
tbl = soup.find('table').find_all('td')
rows = [tbl[x:x + 4] for x in xrange(0, len(tbl), 4)]
result = {}
for r in rows:
uniprot = r[1].text
motif = r[0].text
if uniprot not in result:
result[uniprot] = {}
if motif not in result[uniprot]:
result[uniprot][motif] = []
result[uniprot][motif].append((r[2].text, r[3].text))
return result
[docs]
def elm_classes():
ELMClass = collections.namedtuple(
'ELMClass',
(
'accession',
'identifier',
'functional_name',
'description',
'regex',
'probability',
'n_instances',
'n_pdb',
),
)
url = urls.urls['elm_class']['url']
c = curl.Curl(url, silent = False)
data = c.result
data = [
ELMClass(*x.split('\t'))
for x in data.replace('"', '').split('\n')[6:]
if len(x) > 0
]
return dict(zip(
(x[1] for x in data),
data,
))
[docs]
def elm_instances():
ELMInstance = collections.namedtuple(
'ELMInstance',
(
'accession',
'type',
'identifier',
'uniprot_id',
'uniprot',
'synonyms',
'start',
'end',
'references',
'methods',
'logic',
'pdb',
'organism',
),
)
url = urls.urls['elm_inst']['url']
c = curl.Curl(url, silent = False, slow = True)
data = c.result
data = data.replace('"', '').split('\n')
data = [
x.split('\t')
for x in data[6:]
]
return [
ELMInstance(*x)
for x in data
if len(x) == 13
]
[docs]
def elm_interactions():
"""
Downlods manually curated interactions from ELM.
This is the gold standard set of ELM.
"""
def number_or_none(value, typ = int):
return typ(value) if value != 'None' else None
# UniProt ID with isoform e.g. O14754-1
reupi = re.compile(r'([\w]{6,10})(?:-([0-9]{1,2}))?')
retax = re.compile(r'"([0-9]+)"\([-:/,\.\[\]\(\)\w\s]+\)')
ELMInteraction = collections.namedtuple(
'ELMInteraction',
[
'motif_elm',
'domain_pfam',
'uniprot_motif',
'uniprot_domain',
'isoform_motif',
'isoform_domain',
'start_motif',
'end_motif',
'start_domain',
'end_domain',
'affinity_min',
'affinity_max',
'pubmeds',
'taxon_motif',
'taxon_domain',
],
)
result = []
url = urls.urls['elm_int']['url']
c = curl.Curl(url, silent = False, slow = True)
data = c.result
data = data.split('\n')
del data[0]
for l in data:
if not l:
continue
l = tuple(x.strip() for x in l.split('\t'))
uniprot_mofif, isoform_motif = reupi.match(l[2]).groups()
uniprot_domain, isoform_domain = reupi.match(l[3]).groups()
result.append(
ELMInteraction(
motif_elm = l[0],
domain_pfam = l[1],
uniprot_motif = uniprot_mofif,
uniprot_domain = uniprot_domain,
isoform_motif = int(isoform_motif) if isoform_motif else 1,
isoform_domain = int(isoform_domain) if isoform_domain else 1,
start_motif = int(l[4]),
end_motif = int(l[5]),
start_domain = number_or_none(l[6]),
end_domain = number_or_none(l[7]),
affinity_min = number_or_none(l[8], float),
affinity_max = number_or_none(l[9], float),
pubmeds = tuple(map(int, l[10].split(','))) if l[10] else (),
taxon_motif = int(retax.match(l[11]).groups()[0]),
taxon_domain = int(retax.match(l[12]).groups()[0]),
)
)
return result
