Source code for bioservices.omnipath

# -*- python -*-
#
#  This file is part of bioservices software
#
#  Copyright (c) 2013-2014 - EBI-EMBL
#
#  File author(s):
#      https://github.com/cokelaer/bioservices
#
#  Distributed under the GPLv3 License.
#  See accompanying file LICENSE.txt or copy at
#      http://www.gnu.org/licenses/gpl-3.0.html
#
#  source: http://github.com/cokelaer/bioservices
#  documentation: http://packages.python.org/bioservices
#
##############################################################################
"""Interface to OmniPath web service

.. topic:: What is OmniPath ?

    :URL: http://omnipathdb.org
    :URL: https://github.com/saezlab/pypath/blob/master/webservice.rst

    .. highlights::

        A comprehensive collection of literature curated human signaling pathways.

        -- From OmniPath web site, March 2016


"""
from bioservices import REST
from easydev import to_list 
from bioservices import logger
logger.name = __name__



[docs]class OmniPath(REST): """Interface to the `OmniPath <http://www.ebi.ac.uk/unichem/>`_ service .. doctest:: >>> from bioservices import OmniPath >>> o = OmniPath() >>> net = o.get_network() >>> interactions = o.get_interactions('P00533') """ _url = "http://omnipathdb.org/" def __init__(self, verbose=False, cache=False): """**Constructor** OmniPath :param verbose: set to False to prevent informative messages """ super(OmniPath, self).__init__(name="OmniPath", url=OmniPath._url, verbose=verbose, cache=cache)
[docs] def get_about(self): """Information about the version""" res = self.http_get(self.url + "about").content return res
[docs] def get_network(self, frmt='json'): """Get basic statistics about the whole network including sources""" assert frmt in ['json', 'tsv'] ,"frmt must be set to json or tsv" res = self.http_get(self.url + "network", frmt=frmt, params={'format': frmt}) return res
[docs] def get_interactions(self, query="", frmt='json', fields=[]): """Interactions of proteins :param str query: a valid uniprot identifier (e.g. P00533). It can also be a list of uniprot identifiers, or a string with comma-separated identifiers. :param str fields: additional fields to be added to the output (e.g., sources, references) :param str frmt: format of the output (json or tabular) Example:: res_one = o.get_interactions('P00533') res_many = o.get_interactions('P00533,O15117,Q96FE5') res_many = o.get_interactions(['P00533','O15117','Q96FE5']) res_one = o.get_interactions('P00533', fields='sources') res_one = o.get_interactions('P00533', fields=['source']) res_one = o.get_interactions('P00533', fields=['source', 'references']) You may also keep query to an empty string, but the entire DB will then be downloaded. This may take time and the :attr:`timeout` may need to be increased manually. If frmt is set to TSV, the output is a TSV table with a header. If set to json, a dictionary is returned. """ # make sure there is no spaces if isinstance(query, list): query=",".join(query) else: try: # if input is a string query = query.replace(' ', '') except: pass assert frmt in ['json', 'tsv'] ,"frmt must be set to json or tsv" params = {} params['format'] = frmt from easydev import to_list fields = to_list(fields) if len(fields): params['fields'] = fields #TODO handle multiple fields res = self.http_get(self.url + "interactions/%s" % query, frmt=frmt, params=params) return res
[docs] def get_resources(self, frmt='json'): """Return statistics about the databases and their contents """ res = self.http_get(self.url + "resources", frmt=frmt, params={"format": frmt}) return res
[docs] def get_info(self): """Currently returns HTML page""" from easydev import browser browser.browse(self.url + "info")
[docs] def get_ptms(self, query="", ptm_type=None, frmt='json', fields=[]): """List enzymes, substrates and PTMs :param str query: a valid uniprot identifier (e.g. P00533). It can also be a list of uniprot identifiers, or a string with comma-separated identifiers. :param str ptm_type: restrict the output to this type of PTM (e.g., phosphorylation) :param str fields: additional fields to be added to the output (e.g., sources, references) """ # make sure there is no spaces if isinstance(query, list): query=",".join(query) else: try: # if input is a string query = query.replace(' ', '') except: pass assert frmt in ['json', 'tsv'] ,"frmt must be set to json or tsv" params = {} params['format'] = frmt if len(fields): params['fields'] = fields res = self.http_get(self.url + "ptms/%s" % query, frmt='json', params=params) return res