Ensembl gene centered protein mapping. More...

Inheritance diagram for cls.HSEnsgProteinMapping.CHSEnsgProteinMapping:

Collaboration diagram for cls.HSEnsgProteinMapping.CHSEnsgProteinMapping:

Public Member Functions
def	Convert (s, key, srcDbToken, dstDbToken)
	Map from one database to any other. More...

Public Member Functions inherited from cls.PairwiseMapperBase.CPairwiseMapperBase
def	__init__ (s, paths)
	Constructor. More...

def	GetPaths (s)
	Get CPaths object stored here. More...

Static Public Attributes
	paths = CPaths();

	mapper = CHSEnsgProteinMapping(paths);

Detailed Description

Ensembl gene centered protein mapping.

Mappings are done through Ensembl genes, with very few exceptions. This
has the advantage of noise reduction introduced by alternative
splicing. This class has been implemented in order to facilitate the
switch from gene-centered to protein centered conversions, if needed in
the future. Wherever it is crucial to map directly from one DB to another
without routing through Ensembl genes, an exception mapping is handled.

Member Function Documentation

◆ Convert()

def cls.HSEnsgProteinMapping.CHSEnsgProteinMapping.Convert	(	s,
		key,
		srcDbToken,
		dstDbToken
	)

Map from one database to any other.

    Performs mapping from a source database to a destination database.
    @param key  Identifier to be mapped.
    @param srcDbToken  Database identifier @p key belongs to.
    @param dstDbToken  Database identifier @p key will be mapped to.
    @return A sorted @c list of identifiers. The @c list may be empty,
     this is an indication that there does not exist a mapping between
     the two databases which is routed through the Ensembl database. In
     detail, there can be two reasons:

     - The conversion from the source database to Ensembl cannot be made.
     - The conversion from the Ensembl to the destination db cannot be made.

     In either case, an empty @c list is returned. There remains a small
     chance that a direct mapping can be done without the Ensembl
     intermediate, but this is the price paid for a very generic mapping
     scheme.

Reimplemented from cls.PairwiseMapperBase.CEnsemblMapperBase.

Member Data Documentation

◆ mapper

cls.HSEnsgProteinMapping.CHSEnsgProteinMapping.mapper = CHSEnsgProteinMapping(paths);

static

◆ paths

cls.HSEnsgProteinMapping.CHSEnsgProteinMapping.paths = CPaths();