cls.ReactomeAccess.CReactomeAccess Class Reference

Public Member Functions
def	Initialize (self, config, log=False)
	Initialize the module. More...
def	queryByName (self, name, category=None, operand=OP_AND)
	Query Reactome entries by name(s). More...
def	queryById (self, queryId, idType=None, category=None, siblings=False, children=False, parents=False)
	Query Reactome entries by id(s). More...

Static Public Attributes
	data = None
	entries = None
	iid2iids = None
	xref2iid = None
	iid2xref = None
	parser = None
	config = CPaths()
	react = CReactomeAccess()
	log
list	queries = ["REACT_19257.4", "P01023", "Q13201"]
list	siblings = [True, False, False]
def	results = react.queryById(queries[i], siblings = siblings[i])

Member Function Documentation

Initialize()

def cls.ReactomeAccess.CReactomeAccess.Initialize	(		self,
			config,
			log = False
	)

Initialize the module.

    @param config  @ref common.Paths.CPaths object containing paths
    @param log If @c True will output internal logging information, @c False
    by default.
    @return @c True if all went ok. @c False if there was an error
    (issued by @ref common.ErrorHandler).

queryById()

def cls.ReactomeAccess.CReactomeAccess.queryById	(		self,
			queryId,
			idType = None,
			category = None,
			siblings = False,
			children = False,
			parents = False
	)

Query Reactome entries by id(s).

   @param queryId Query identifier(s), either a single id or multiple
   ids in a set or list.
   @param idType Type of the identifier, e.g. UniProt or Reactome.
   @param category Reactome category to limit the search, e.g. Protein or
   Pathway. Can be either a single string, a set/list of multiple
   categories, or None if all categories should be included.
   @param siblings If @c True, all entries that are annotated with the
   same id are also included. Only useful if the query id is a Reactome ID
   of e.g. a Pathway or a BiochemicalReaction. Can be used to only retrieve
   those Reactome entries, where certain panel protein/genes are
   participating. @c False by default/
   @param children If @c True, the Reactome pathway hierarchy will be
   traversed and all entries descending from the query id will be included.
   In case of a query by Reactome pathway id, this would include all the
   reactions and the participating entities. A query by UniProt or a
   Reactome small molecule identifier would not include anything more,
   as those entries are the lowest in the pathway tree. @c False by default.
   @param parents If @c True, the Reactome pathway hierarchy will be
   traversed and all entries ascending from the query id will be included.
   In case of a query by Uniprot or Reactome protein id, this would include
   all the reactions and pathways those entries are participating in, a
   query by Reactome biochemical reaction id would include all the pathways
   this reaction is listed in. A query by Reactome pathway id would not
   ascend further, as this is the highest level in the pathway tree. @c
   False by default.
   @return A list of Reactome entries that fulfil the query criteria. @c
   False, if there was an error (issued by @ref common.ErrorHandler).

queryByName()

def cls.ReactomeAccess.CReactomeAccess.queryByName	(		self,
			name,
			category = None,
			operand = OP_AND
	)

Query Reactome entries by name(s).

   @param name Query name, either a single string or multiple query strings
   in a set or list.
   @param category Reactome category to limit the search, e.g. Protein or
   Pathway. Can be either a single String, a set/list of multiple
   categories, or None if all categories should be queried.
   @param operand How to combine the query string if it contains multiple
   entries, either AND (union) or OR (intersection).
   @return A list of Reactome entries that fulfil the query criteria. @c
   False, if there was an error (issued by @ref common.ErrorHandler).

Member Data Documentation

config

cls.ReactomeAccess.CReactomeAccess.config = CPaths()

static

data

cls.ReactomeAccess.CReactomeAccess.data = None

static

entries

cls.ReactomeAccess.CReactomeAccess.entries = None

static

iid2iids

cls.ReactomeAccess.CReactomeAccess.iid2iids = None

static

iid2xref

cls.ReactomeAccess.CReactomeAccess.iid2xref = None

static

log

cls.ReactomeAccess.CReactomeAccess.log

static

parser

cls.ReactomeAccess.CReactomeAccess.parser = None

static

queries

list cls.ReactomeAccess.CReactomeAccess.queries = ["REACT_19257.4", "P01023", "Q13201"]

static

react

cls.ReactomeAccess.CReactomeAccess.react = CReactomeAccess()

static

results

def cls.ReactomeAccess.CReactomeAccess.results = react.queryById(queries[i], siblings = siblings[i])

static

siblings

list cls.ReactomeAccess.CReactomeAccess.siblings = [True, False, False]

static

xref2iid

cls.ReactomeAccess.CReactomeAccess.xref2iid = None

static

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The documentation for this class was generated from the following file:

• cls/ReactomeAccess.py