Base class for Ensembl-centric mappings and conversions. More...
Inheritance diagram for cls.PairwiseMapperBase.CEnsemblMapperBase:
Collaboration diagram for cls.PairwiseMapperBase.CEnsemblMapperBase:
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... | |
Detailed Description
Base class for Ensembl-centric mappings and conversions.
As Ensembl with its Biomart tables is a rather important and central database in our system, this class defines an interface for doing simple mappings.
Member Function Documentation
◆ Convert()
| def cls.PairwiseMapperBase.CEnsemblMapperBase.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 in cls.HSEnsgProteinMapping.CHSEnsgProteinMapping.
The documentation for this class was generated from the following file:
