#!/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 pypath.resources.urls as urls
import pypath.share.curl as curl
import pypath.inputs.mitab as mitab
import pypath.share.cache as _cache
[docs]
def dip_interactions(
url = None,
organism = 9606,
core_only = True,
direct_only = True,
small_scale_only = True,
):
strDipCore = 'dip-quality-status:core'
strDirect = 'direct interaction'
strPhysInt = 'physical interaction'
strSmallS = 'small scale'
url = (
url or
(urls.urls['dip']['url_rescued'] % ('CR' if core_only else ''))
)
c = curl.Curl(url, silent = False, large = True)
f = c.result
i = []
lnum = 0
for l in f:
if lnum == 0:
lnum += 1
continue
l = l.replace('\n', '').replace('\r', '')
l = l.split('\t')
specA = int(l[9].split(':')[1].split('(')[0])
specA = 0 if l[9] == '-' else int(l[9].split(':')[1].split('(')[0])
specB = 0 if l[10] == '-' else int(l[10].split(':')[1].split('(')[0])
intProp = mitab.mitab_field_list(l[11])
intProc = mitab.mitab_field_list(l[15])
dipLinkId = l[13]
expEv = mitab.mitab_field_list(l[6])
conf = l[14]
if organism is None or (specA == organism and specB == organism):
if (
(
not core_only or
strDipCore in conf
) and (
not direct_only or
strDirect in intProp or
strPhysInt in intProp
) and (
not small_scale_only or
strSmallS in intProc
)
):
pm = l[8].replace('pubmed:', '').split('|')
pm = [p for p in pm if not p.startswith('DIP')]
l = [l[0], l[1]]
uniprotA = mitab.mitab_field_uniprot(l[0])
uniprotB = mitab.mitab_field_uniprot(l[1])
if uniprotA and uniprotB:
i.append([
uniprotA,
uniprotB,
';'.join(pm),
';'.join(intProp),
';'.join(expEv),
dipLinkId,
])
lnum += 1
f.close()
return i
[docs]
def dip_login(user, passwd):
"""
This does not work for unknown reasons.
In addition, the binary_data parameter of Curl().__init__() has been
changed, below updates are necessary.
"""
bdr = '---------------------------8945224391427558067125853467'
useragent = 'Mozilla/5.0 (X11; U; Linux i686; en-US; rv:43.0) '\
'Gecko/20110304 Firefox/43.0'
loginfname = os.path.join(_cache.get_cachedir(), 'dip.logindata.tmp')
url = urls.urls['dip']['login']
req_hdrs = ['User-Agent: %s' % useragent]
c = curl.Curl(
url,
cache = False,
write_cache = False,
req_headers = req_hdrs,
return_headers = True,
debug = True)
res = c.result
hdr = c.resp_headers
cookie = hdr['set-cookie'].split(';')[0]
cookie2 = '%s%u' % (cookie[:-1], int(cookie[-1]) + 1)
othercookie = 'DIPID=11133%3A'
req_hdrs = [
'Content-type: multipart/form-data; '
'boundary = %s' % bdr,
'Cookie: %s' % cookie2,
'Referer: %s' % url,
'User-Agent: %s' % useragent,
'Connection: keep-alive',
]
post = {'lgn': '1', 'login': user, 'pass': passwd, 'Login': 'Login'}
login = '--%s\r\n\r\nContent-Disposition: form-data; name = "lgn"\r\n\r\n1'\
'\r\n--%s\r\n\r\nContent-Disposition: form-data; name = "login"\r\n\r\n'\
'%s\r\n--%s\r\n\r\nContent-Disposition: form-data; name = "pass"\r\n\r'\
'\n%s\r\n--%s\r\n\r\nContent-Disposition: form-data; name = "Login"\r\n'\
'\r\nLogin\r\n%s--\r\n' % (bdr, bdr, user, bdr, passwd, bdr, bdr)
# login = login.replace('\r', '')
with codecs.open(loginfname, encoding = 'ISO-8859-1', mode = 'w') as f:
f.write(login)
c = curl.Curl(
url,
cache = False,
write_cache = False,
follow = True,
req_headers = req_hdrs,
timeout = 10,
binary_data = loginfname,
return_headers = True,
debug = True)
res = c.result
hdr = c.resp_headers
return res, hdr
