cls.GenericGeneIdConverter Namespace Reference

Command line implementation for conversion between different gene IDs. More...

Functions
def	HandleGeneIdConversion (cnvCls, argParser, columnNames, format2DB)
	Command line conversion of gene IDs. More...

Detailed Description

Command line implementation for conversion between different gene IDs.

Author

Chris X. Weichenberger

Date

2012-09-21

Copyright

See LICENSE file.

Function Documentation

HandleGeneIdConversion()

def cls.GenericGeneIdConverter.HandleGeneIdConversion	(		cnvCls,
			argParser,
			columnNames,
			format2DB
	)

Command line conversion of gene IDs.

This function is a generic command line tool for converting gene IDs
within a species. It provides a command line interface and leaves open the
conversion to a specialized object that derives from
@c cls.PairwiseMapperBase.CPairwiseMapperBase. It implements a simple, but
@c general rule. One gene ID is mapped to another gene ID through a
central 'hub' gene ID, preferably an Ensembl gene ID. Each ID can be
mapped to each other, there are no special options that can be applied to
a certain conversion.
@param  cnvCls  Class capable of doing the gene id conversion. Should be a
 derived class from @c cls.PairwiseMapperBase.CPairwiseMapperBase.
@param  argParser @c cls.ArgumentParserBase.CArgumentParserBase instance
 which has been initialized with the description of the species' gene
 conversion possibilities.
@param  columnNames A @c dictionary which provides clear text to headers
 generated by the conversion. Key is the gene ID token, value is the
 header text.
@param  format2DB A @c dictionary with the same gene ID tokens for keys as
 the previous dictionary. Values are the database tokens defined in @c
 common.Globals. This dictionary establishes a link between the gene
 translation table and the input/output option specified in the command
 line.