tacco.tools.setup_orthology_converter

setup_orthology_converter(homology_file='http://www.informatics.jax.org/downloads/reports/HOM_AllOrganism.rpt', working_directory='.')[source]

Setup for converting gene names between species using MGI homology information (Mouse Genome Informatics Web Site, http://www.informatics.jax.org/homology.shtml).

Parameters:

  • homology_file – File containing a mapping from species specific gene symbols to common MGI “DB class key”/”HomoloGene ID”, e.g. downloaded from http://www.informatics.jax.org/downloads/reports/HOM_AllOrganism.rpt. If this is not available as a local file, it is treated as an URL and downloaded to the working_directory if necessary, see below.

  • working_directory – Directory where to buffer downloaded files. If a file of the same name already exists in this directory, it is not downloaded again.

Returns:

A string containing the local path to the homology file.