def __init__(self, verbose=False, cache=False):
""".. rubric:: Constructor
:param bool verbose: prints informative messages (default is off)
"""
url = "http://www.rcsb.org/pdb/rest"
self.services = REST(name="PDB", url=url, verbose=verbose, cache=cache)
def __init__(self, verbose=False, cache=False):
"""**Constructor**
"""
self.services = REST(name="cog",
url=COG._url,
verbose=verbose,
cache=cache)
def __init__(self, verbose=True):
""".. rubric:: Constructor
:param bool verbose:
"""
url = "https://www.ebi.ac.uk/Tools/services/rest/emboss_seqret"
self.services = REST(name="seqret", url=url, verbose=verbose)
self._parameters = None
def __init__(self, verbose=False):
url = "http://www.ebi.ac.uk/Tools/services/rest/muscle"
self.services = REST(name='MUSCLE', url=url, verbose=verbose)
self._parameters = None
self._parametersDetails = {}
self._headers = {
"User-Agent": self.services.getUserAgent(),
"accept": "application/json"
}
def __init__(self, verbose=False, cache=False):
"""**Constructor**
:param verbose: set to False to prevent informative messages
"""
self.services = REST(name="ENA",
url=ENA.url,
verbose=verbose,
cache=cache)
self.services.TIMEOUT = 100
def __init__(self, verbose=False):
""".. rubric:: NCBIblast constructor
:param bool verbose: prints informative messages
"""
url = "http://www.ebi.ac.uk/Tools/services/rest/ncbiblast"
self.services = REST(name="NCBIblast", url=url, verbose=verbose)
self._parameters = None
self._parametersDetails = {}
self.checkInterval = 2
def __init__(self, verbose=False, cache=False):
""".. rubric:: Constructor
:param bool verbose: prints informative messages (default is off)
"""
self.services = REST(name="PDB",
verbose=verbose,
cache=cache,
url_defined_later=True)
self.services.url = PDB._url
def __init__(self, verbose=True, cache=False):
""".. rubric:: Constructor
:param bool verbose: prints informative messages
"""
self.easyXMLConversion = False
self._default_extension = "json"
self.services = REST(name='PathwayCommons', url=PathwayCommons._url,
verbose=verbose, cache=cache)
def __init__(self, verbose=True, cache=False):
""".. rubric:: Constructor
:param bool verbose:
"""
self.services = REST(name="BioDBNet",
url=BioDBNet._url,
verbose=verbose,
cache=cache)
self._valid_inputs = self.getInputs()
def __init__(self, verbose=False, cache=False):
""".. rubric:: Constructor
:param bool verbose: prints informative messages (default is off)
"""
url = "https://www.ebi.ac.uk/pdbe/api/pdb/entry/"
self.services = REST(name="PDBe",
url=url,
verbose=verbose,
cache=cache)
def __init__(self, verbose=False, cache=False):
""".. rubric:: Constructor
:param bool verbose: prints informative messages (default is off)
"""
url = "https://mygene.info/v3"
self.services = REST(name="PDBe",
url=url,
verbose=verbose,
cache=cache)
def __init__(self, verbose=False, cache=False):
""".. rubric:: Constructor
:param bool verbose: prints informative messages
"""
self.services = REST(name="ArrayExpress",
url="http://www.ebi.ac.uk/arrayexpress",
cache=cache,
verbose=verbose)
self.version = "v2"
def __init__(self, verbose=True, cache=False):
"""**Constructor**
:param verbose: set to False to prevent informative messages
"""
#super(Panther, self).__init__(name="Panther", url=Panther._url,
# verbose=verbose, cache=cache)
self.services = REST(name="Panther",
url=Panther._url,
verbose=verbose,
cache=cache)
self._allPathwaysURL = "http://www.pantherdb.org/pathway/pathwayList.jsp"
def __init__(self, verbose=True, cache=False):
""".. rubric:: Rhea constructor
:param bool verbose: True by default
::
>>> from bioservices import Rhea
>>> r = Rhea()
"""
self.services = REST(name="Rhea",
url=Rhea._url,
verbose=verbose,
cache=cache)
def __init__(self, verbose=True, cache=False):
"""**Constructor**
:param verbose: set to False to prevent informative messages
"""
self.services = REST(name="BioCarta",
url=BioCarta._url,
cache=cache,
verbose=verbose)
self.fname = "biocarta_pathways.txt"
self._organism = None
self._organism_prefix = None
self._pathways = None
def __init__(self, version="1.0", verbose=True, cache=False):
""".. rubric:: Rhea constructor
:param str version: the current version of the interface (1.0)
:param bool verbose: True by default
::
>>> from bioservices import Rhea
>>> r = Rhea()
"""
self.services = REST(name="Rhea",
url=Rhea._url,
verbose=verbose,
cache=cache)
self.version = version
self.format_entry = ["cmlreact", "biopax2", "rxn"]
def __init__(self, verbose=False, cache=False):
# http://bigg.ucsd.edu/data_access
self.services = REST(name="BiGG",
url=BiGG._url, cache=cache, requests_per_sec=10,
verbose=verbose)
def __init__(self, verbose=True, cache=False):
self.services = REST(name="Reactome",
url=Reactome._url,
verbose="ERROR",
cache=False)
self.debugLevel = verbose