Genemap

Genemap is a python library for mapping (gene) identifiers. Genemaps main purpose is provide an easy approach for mapping (gene) identifers from one identifier type to another, which is unfortunately often not a trivial task. This may be useful for translating identifiers into a format that you are more familiar with (such as gene symbols instead of Ensembl IDs) or even for translating between different species (e.g., from mouse IDs to human IDs) to compare datasets or annotations between species.

Genemap currently supports the following mappings:

• EnsemblMapper - Translates identifiers using Ensembl via Biomart. Supports mapping between various types of gene identifiers that are present in Ensembl (gene symbols, Ensembl/Entrez identifiers, e.g.) and between different species (using orthologous genes).
• MgiMapper - Translates identifers using the homology table provided by MGI. Supports mapping between gene symbols and Entrez identifers and between several specifies (using orthologous genes).
• CustomMapper - Translates identifiers using a custom mapping provided by the user. The nature of the performed mapping depends on the provided mapping table.

For a complete overview of the provided mappers and their basic usage, see the the Overview and Usage sections. More details on the API are available in the API section. Finally, for an overview of genemaps command line usage, see the Command line section.