cls.MITABAccess.CMITABAccess Class Reference

Parses and stores the content of a MITAB file for later querying. More...

Public Member Functions
def	Initialize (self, config, parserConfig=None)
	Initialize module. More...
def	GetSignificanceOfInteractionOverlap (self, queryId, setIds)
	Compute likelihood ratio and p-value for the overlap of interactions annotated to the query id and the set ids. More...
def	GetInteractionsByID (self, queryIds=None, targetIds=None)
def	GetStats (self)

Static Public Attributes
	data = defaultdict(dict)
	mapperProt = None
	mapperGene = None
	skippedOrganisms = defaultdict(set)
	skippedLines = defaultdict(str)
	includedLines = set()
	starttime = time.time()
	config = CPaths()
	mitab = CMITABAccess()
	conf2 = CMitabParserParams(mapIdentifiers = False)
def	stats = mitab.GetStats()

Detailed Description

Parses and stores the content of a MITAB file for later querying.

Depending on the chosen parameters can be quite memory intense.

Member Function Documentation

GetInteractionsByID()

def cls.MITABAccess.CMITABAccess.GetInteractionsByID	(		self,
			queryIds = None,
			targetIds = None
	)

     Get all the interactions that are known for the id provided.

     @param queryId The identifier
     @return A list of interactions

GetSignificanceOfInteractionOverlap()

def cls.MITABAccess.CMITABAccess.GetSignificanceOfInteractionOverlap	(		self,
			queryId,
			setIds
	)

Compute likelihood ratio and p-value for the overlap of interactions annotated to the query id and the set ids.

In contrast to GetInteractionsByID, this method does not return any interactions that involve queryId and setIds, but will use these to compute the significance of the overlap, considering all interactions as the background. The likelihood ratio and pvalue are computed using Fisher's exact test

Parameters

queryId	The id of the query interactors
setIds	THe ids of the interactors annotated to a certain set

Returns

A tuple containing likelihood ratio, p-value

GetStats()

def cls.MITABAccess.CMITABAccess.GetStats

(

self

)

     Returns some statistics  in the input file like the total number
     of PPI, complexes, etc.

     @return A dictionary containing information

Initialize()

def cls.MITABAccess.CMITABAccess.Initialize	(		self,
			config,
			parserConfig = None
	)

Initialize module.

    @param config  @ref common.Paths.CPaths object containing information on
    where to find the data
    @param parserConfig Additional parameters that defined, which type of
    interactions we are working with. Can be omitted, in which case default
    parameters will be used.
    @return @c True if all went ok. @c False if there was an error
    (issued by @ref ErrorHandler).

Member Data Documentation

conf2

cls.MITABAccess.CMITABAccess.conf2 = CMitabParserParams(mapIdentifiers = False)

static

config

cls.MITABAccess.CMITABAccess.config = CPaths()

static

data

cls.MITABAccess.CMITABAccess.data = defaultdict(dict)

static

includedLines

cls.MITABAccess.CMITABAccess.includedLines = set()

static

mapperGene

cls.MITABAccess.CMITABAccess.mapperGene = None

static

mapperProt

cls.MITABAccess.CMITABAccess.mapperProt = None

static

mitab

cls.MITABAccess.CMITABAccess.mitab = CMITABAccess()

static

skippedLines

cls.MITABAccess.CMITABAccess.skippedLines = defaultdict(str)

static

skippedOrganisms

cls.MITABAccess.CMITABAccess.skippedOrganisms = defaultdict(set)

static

starttime

cls.MITABAccess.CMITABAccess.starttime = time.time()

static

stats

def cls.MITABAccess.CMITABAccess.stats = mitab.GetStats()

static

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

• cls/MITABAccess.py