def __init__(self, organism='H**o sapiens', verbose=True, cache=False):
""".. rubric:: Constructor
:param str orgamism: the organism to look at. H**o sapiens
is the default. Other possible organisms can be found
in :attr:`organisms`.
:param str verbose: a verbose level in ERROR/DEBUG/INFO/WARNING
compatible with those used in BioServices.
"""
super(Complexes, self).__init__(level=verbose)
self.devtools = DevTools()
self.webserv = IntactComplex(verbose=verbose, cache=cache)
df = self.webserv.search('*', frmt='pandas')
self.df = df
#: list of valid organisms found in the database
self.valid_organisms = list(set(df['organismName']))
self.valid_organisms = [x.split(';')[0] for x in self.valid_organisms]
#: list of valid organisms found in the database
self.organisms = list(set(df['organismName']))
self._organism = None
if organism in self.organisms:
self.organism = organism
else:
print("Organism not set yet. ")
# This will populated on request as a cache/buffer
self._details = None
self._complexes = None
def __init__(self, organism="H**o sapiens", cache=False):
""".. rubric:: Constructor
:param str orgamism: the organism to look at. H**o sapiens
is the default. Other possible organisms can be found
in :attr:`organisms`.
"""
self.logging = Logging()
self.devtools = DevTools()
self.webserv = IntactComplex(verbose=verbose, cache=cache)
df = self.webserv.search("*", frmt="pandas")
self.df = df
#: list of valid organisms found in the database
self.valid_organisms = list(set(df["organismName"]))
self.valid_organisms = [x.split(";")[0] for x in self.valid_organisms]
#: list of valid organisms found in the database
self.organisms = list(set(df["organismName"]))
self._organism = None
if organism in self.organisms:
self.organism = organism
else:
print("Organism not set yet. ")
# This will populated on request as a cache/buffer
self._details = None
self._complexes = None
class Complexes(Logging):
"""Manipulate complexes of Proteins
This class uses Intact Complex database to extract information about
complexes of proteins.
When creating an instance, the default organism is "H**o sapiens".
The organism can be set to another one during the instanciation or later::
>>> from biokit.network.complexes import Complexes
>>> c = Complexes(organism='H**o sapiens')
>>> c.organism = 'Rattus norvegicus'
Valid organisms can be found in :attr:`organisms`. When changing the
organism, a request to the Intact database is sent, which may take some
time to update. Once done, information related to this organism is stored
in the :attr:`df` attribute, which is a Pandas dataframe. It
contains 4 columns. Here is for example one row::
complexAC EBI-2660609
complexName COP9 signalosome variant 1
description Essential regulator of the ubiquitin (Ubl) con...
organismName H**o sapiens; 9606
This is basic information but once a complex accession (e.g., EBI-2660609)
is known, you can retrieve detailled information. This is done
automatically for all the accession when needed. The first time, it will
take a while (20 seconds for 250 accession) but will be cache for this
instance.
The :attr:`complexes` contains all details about the entries found in
:attr:`df`. It is a dictionary where keys are the complex accession. For
instance::
>>> c.complexes['EBI-2660609']
In general, one is interested in the participants of the complex, that is
the proteins that form the complex. Another attribute is set for you::
>>> c.participants['EBI-2660609']
Finally, you may even want to obtain just the identifier of the participants
for each complex. This is stored in the :attr:`identifiers`::
>>> c.identifiers['EBI-2660609']
Note however, that the identifiers are not neceseraly uniprot identifiers.
Could be ChEBI or sometimes even set to None. The :meth:`strict_filter`
removes the complexes with less than 2 (strictly) uniprot identifiers.
Some basic statistics can be printed with :meth:`stats` that indeticates
the number of complexes, number of identifiers in those complexes ,and
number of unique identifiers. A histogram of number of appearance of each
identifier is also shown.
The :meth:`hist_participants` shows the number of participants per complex.
Finally, the meth:`search_complexes` can be used in the context of
logic modelling to infer the AND gates from a list of uniprot identifiers
provided by the user. See :meth:`search_complexes` for details.
Access to the Intact Complex database is performed using the
package BioServices provided in Pypi.
"""
def __init__(self, organism='H**o sapiens', verbose=True, cache=False):
""".. rubric:: Constructor
:param str orgamism: the organism to look at. H**o sapiens
is the default. Other possible organisms can be found
in :attr:`organisms`.
:param str verbose: a verbose level in ERROR/DEBUG/INFO/WARNING
compatible with those used in BioServices.
"""
super(Complexes, self).__init__(level=verbose)
self.devtools = DevTools()
self.webserv = IntactComplex(verbose=verbose, cache=cache)
df = self.webserv.search('*', frmt='pandas')
self.df = df
#: list of valid organisms found in the database
self.valid_organisms = list(set(df['organismName']))
self.valid_organisms = [x.split(';')[0] for x in self.valid_organisms]
#: list of valid organisms found in the database
self.organisms = list(set(df['organismName']))
self._organism = None
if organism in self.organisms:
self.organism = organism
else:
print("Organism not set yet. ")
# This will populated on request as a cache/buffer
self._details = None
self._complexes = None
def _get_organism(self):
return self._organism
def _set_organism(self, organism):
self.devtools.check_param_in_list(organism, [str(x.split(";")[0]) for x in self.valid_organisms])
self._organism = organism
self.df = self.webserv.search('*', frmt='pandas',
filters='species_f:("%s")' % self.organism)
self._complexes = None
organism = property(_get_organism, _set_organism,
doc="Getter/Setter of the organism")
def hist_participants(self):
"""Histogram of the number of participants per complexes
:return: a dictionary with complex identifiers as keys and
number of participants as values
::
from biokit.network.complexes import Complexes
c = Complexes()
c.hist_participants()
"""
N = []
count = {}
for i, identifier in enumerate(self.complexes.keys()):
n = len(self.complexes[identifier]['participants'])
N.append(n)
count[identifier] = n
_ = pylab.hist(N, bins=range(0, max(N)))
pylab.title('Number of participants per complex')
pylab.grid()
return count
def stats(self):
"""Prints some stats about the number of complexes and histogram of the
number of appearances of each species"""
species = []
for k in self.participants.keys():
species.extend([x['identifier'] for x in self.participants[k]])
N = []
for spec in set(species):
N.append(species.count(spec))
_ = pylab.hist(N, bins=range(0, max(N)))
pylab.title("Number of appaerances of each species")
pylab.grid()
print("""There are %s complexes involving %s participants with %s unique species. """ %
(len(self.complexes), len(species), len(set(species))))
def _get_participants(self):
participants = {}
for k,v in self.complexes.items():
participants[k] = v['participants']
return participants
participants = property(_get_participants,
doc="""Getter of the complex participants (full details)""")
def _get_identifiers(self):
identifiers = {}
for k,v in self.participants.items():
identifiers[k] = [x['identifier'] for x in v]
return identifiers
identifiers = property(_get_identifiers,
doc="""Getter of the identifiers of the complex participants""")
def _get_complexes(self):
if self._complexes is None:
self._load_complexes()
return self._complexes.copy()
complexes = property(_get_complexes,
doc="""Getter of the complexes (full details""")
def _load_complexes(self, show_progress=True):
from easydev import Progress
import time
pb = Progress(len(self.df.complexAC))
complexes = {}
self.logging.info("Loading all details from the IntactComplex database")
for i, identifier in enumerate(self.df.complexAC):
res = self.webserv.details(identifier)
complexes[identifier] = res
if show_progress:
pb.animate(i+1)
self._complexes = complexes
def remove_homodimers(self):
"""Remove identifiers that are None or starts with CHEBI
and keep complexes that have at least 2 participants
:return: list of complex identifiers that have been removed.
"""
# None are actually h**o dimers
toremove = []
for k,this in self.identifiers.items():
remains = [x for x in this if x is not None]
if len(remains)<=1:
toremove.append(k)
self.logging.info("removing %s homodimers complexes" % len(toremove))
for this in toremove:
del self._complexes[this]
return toremove
def search_complexes(self, user_species, verbose=False):
"""Given a list of uniprot identifiers, return complexes and
possible complexes.
:param list user_species: list of uniprot identifiers to be
found in the complexes
:return: two dictionaries. First one contains the complexes
for which all participants have been found in the user_species
list. The second one contains complexes for which some participants
(not all) have been found in the user_species list.
"""
level = self.debugLevel[:]
if verbose:
self.debugLevel = 'INFO'
else:
self.debugLevel = 'ERROR'
and_gates = {}
candidates = {}
identifiers = self.identifiers.values()
for k, identifiers in self.identifiers.items():
# get rid of suffixes such as -1 or -PRO_xxx
prefixes = [x.split("-")[0] if x is not None else x for x in identifiers]
# You may have a complex with ['P12222', 'P33333-PRO1',
# 'P33333-PRO2'], in which case P33333 is found only once and
# thereofre the final number of found participants is not the length
# of the complexes...so we need to get rid of the duplicates if any
prefixes = list(set(prefixes))
N = len(prefixes)
found = [spec for spec in user_species if spec in prefixes]
if len(found) == N:
self.logging.info('Found entire complex %s ' % k)
and_gates[k] = identifiers[:]
elif len(found) >= 1:
self.logging.info('Found partial complex %s with %s participants out of %s' %
(k, len(found), len(identifiers)))
candidates[k] = {'participants': identifiers, 'found': found}
self.debugLevel = level[:]
return and_gates, candidates
def search(self, name):
"""Search for a unique identifier (e.g. uniprot) in all complexes
:return: list of complex identifiers where the name was found
"""
found = []
for k, identifiers in self.identifiers.items():
prefixes = [x.split("-")[0] if x is not None else x for x in identifiers ]
if name in prefixes:
self.logging.info("Found %s in complex %s (%s)" % (name, k,
identifiers))
found.append(k)
return found
def chebi2name(self, name):
"""Return the ASCII name of a CHEBI identifier"""
from bioservices import ChEBI
c = ChEBI()
name = dict(c.getLiteEntity(name)[0])['chebiAsciiName']
return name
def uniprot2genename(self, name):
"""Return the gene names of a UniProt identifier"""
from bioservices import UniProt
c = UniProt(cache=True)
try:
res = pd.read_csv(StringIO(c.search(name, limit=1)), sep='\t')
return list(res['Gene names'].values)
except:
print("Could not find %s" % name)
def report(self, species):
complete, partial = self.search_complexes(species, verbose=False)
res = {'Found':[], 'Participants':[], 'Complete':[],
'Identifier':[], 'Number found':[], 'Number of participants':[],
'Name':[]}
for k, v in complete.items():
res['Name'].append(self.complexes[k]['name'])
res['Found'].append(";".join(v))
res['Number found'].append(len(v))
res['Participants'].append(";".join(self.identifiers[k]))
res['Number of participants'].append(len(self.identifiers[k]))
res['Complete'].append(True)
res['Identifier'].append(k)
for k, v in partial.items():
res['Name'].append(self.complexes[k]['name'])
res['Found'].append(";".join(v['found']))
res['Number found'].append(len(v['found']))
res['Participants'].append(";".join(self.identifiers[k]))
res['Number of participants'].append(len(self.identifiers[k]))
res['Complete'].append(False)
res['Identifier'].append(k)
res = pd.DataFrame(res, columns=['Found', 'Participants', 'Identifier', 'Name', 'Number found',
'Number of participants', 'Complete'])
return res
# -*- coding: utf-8 -*-
"""
Created on Fri Aug 11 00:40:21 2017
@author: moghb
"""
import json
import requests
import logging
from bioservices import IntactComplex
import os
your_project_directory="C:\\Users\\moghb\\OneDrive\\Documents\\Database\\expert_schema"
s = IntactComplex()
r=s.search('nup53')['elements'][0]['complexAC']
logger = logging.getLogger(__name__)
url ="https://www.ebi.ac.uk/intact/complex-ws/details/"+r+"?format=json"
def do_request_complexdb( ):
resp = requests.get(url)
logger.debug('Requested {}'.format(resp.url))
if resp.status_code == 200:
return resp
else:
raise Exception(resp)
j = json.loads(do_request_complexdb().text)
with open(os.path.join(your_project_directory, 'data.txt'), 'w') as outfile:
