How to use the bioservices.logger function in bioservices

BioGRID is an online interaction repository with data compiled through
        comprehensive curation efforts. Our current index is version 3.2.97 and searches
        37,954 publications for 638,453 raw protein and genetic interactions from major
        model organism species. All interaction data are freely provided through our
        search index and available via download in a wide variety of standardized
        formats.

        -- From BioGrid website, Feb. 2013

"""
from __future__ import print_function

from bioservices import PSICQUIC
import re
from bioservices import logger
logger.name = __name__


__all__ = ["BioGRID"]


class Search(PSICQUIC):
    """ Class that carries out the actual search via psicquic.


    .. todo:: to be removed"""

    def __init__(self, data):
        super(Search, self).__init__(verbose="ERROR")
        self.data = data
        if "biogrid" in self.activeDBs:
            self.output = self.query("biogrid",self.data)

.. mapping between uniprot and bunch of other DBs.
.. ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/
.. http://www.uniprot.org/docs/speclist
.. http://www.uniprot.org/docs/pkinfam

"""
from __future__ import print_function
import types
import io
import sys

from bioservices.services import REST
from bioservices import logger
logger.name = __name__

try:
    import pandas as pd
except:
    pass
__all__ = ["UniProt"]

# TODO:: falt files to get list of identifiers
# http://www.ebi.ac.uk/uniprot/database/download.html
# grep sp uniprot_sprot.fasta  | grep HUMAN | awk '{print substr($1, 12, length($1))}'

mapping = {"UniProtKB AC/ID": "ACC+ID",
           "UniProtKB": "ACC",
           "UniProtKB": "ID",
           "UniParc": "UPARC",
           "UniRef50": "NF50",

"NCBI BLAST - Protein Database Query

        The emphasis of this tool is to find regions of sequence similarity,
        which will yield functional and evolutionary clues about the structure
        and function of your novel sequence."

        -- from NCBIblast web page


"""
import sys
import time

from bioservices.services import REST
from bioservices import logger
logger.name = __name__


__all__ = ["NCBIblast"]


class NCBIblast(REST):
    """Interface to the `NCBIblast `_ service.


    ::

        >>> from bioservices import *
        >>> s = NCBIblast(verbose=False)
        >>> jobid = s.run(program="blastp", sequence=s._sequence_example,
            stype="protein", database="uniprotkb", email="name@provider")
        >>> s.getResult(jobid, "out")

identifier and "gene" is the gene identifier, usually locus_tag or ncbi GeneID, or the primary
gene name.


"""
from __future__ import print_function
from __future__ import unicode_literals
try:
    from functools import reduce # python3 compat
except:
    pass
from bioservices.services import REST, BioServicesError
import webbrowser
import copy
from bioservices import logger
logger.name = __name__


from easydev.logging_tools import Logging

__all__ = ["KEGG",  "KEGGParser"]


class KEGG(REST):
    """Interface to the `KEGG `_ service

    This class provides an interface to the KEGG REST API. The weblink tools
    are partially accesible. All dbentries can be parsed into dictionaries using
    the :class:`KEGGParser`

    Here are some examples. In order to retrieve the entry of the 
    gene identifier 7535 of the **hsa** organism, type::

The European Nucleotide Archive (ENA) provides a comprehensive
        record of the world's nucleotide sequencing information, covering
        raw sequencing data, sequence assembly information and functional
        annotation.

        -- From ENA web page Jan 2016

.. versionadded:: 1.4.4

"""
import os
from bioservices.services import REST
import webbrowser
from bioservices import logger
logger.name = __name__


__all__ = ["ENA"]


class ENA(REST):
    """Interface to `ChEMBL `_

    Here is a quick example to retrieve a target given its ChEMBL Id

    .. doctest::

        >>> from bioservices import ChEMBL
        >>> s = ENA(verbose=False)

: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__



class OmniPath(REST):
    """Interface to the `OmniPath `_ service

    .. doctest::

            >>> from bioservices import OmniPath
            >>> o = OmniPath()
            >>> net = o.get_network()
            >>> interactions = o.get_interactions('P00533')

    """

    _url = "http://omnipathdb.org/"