gi2taxonomy seems outdated

[bernt-matthias]

The tool depends on package_taxonomy_1_0_0 which seems to be replaced by data_manager_fetch_ncbi_taxonomy.

Furthermore the data for the tool data is hard coded in the python file: see GI2TAX, NAME_FILE, NODE_FILE. It would be nice if

• GI2tax could be taken from tool data of gi2taxonomy or the history and
• the latter two somehow provided by the data_manager_fetch_ncbi_taxonomy.

This would be nice because the tool could then map arbitrary IDs (e.g. uniprot ids) to the taxonomy, given a mapping from the IDs to NCBI taxids.

One could also thing about to simplify the tool such that it creates the table only from the taxids and the mapping from the gi (or other ids) could be done with other tools (e.g. join).