File file indicating path to all GTDB genomes
donovan-h-parks opened this issue · 5 comments
It would be nice to have an export function (perhaps in the 'metadata' menu) that allowed a flat file to be dumped indicating the absolute path to all genome directories currently in the GTDB. It is a bit non-trivial to get this at the moment given that genomes are stored in both user directories, RefSeq directories, and Genbank directories. This file would be useful for a number of downstream applications that need a way to access the genomic data of all genomes in the GTDB at a specific point in time.
This has been implemented and will be released in the next GTDB version
What menu did you put this under? It could probably go under the "power" menu as it isn't going to be of interest outside of developers.
For the moment, The command is under metadata export:
gtdb metadata export --path --output /tmp/path_to_del.txt
It can be moved if required.
On 5/04/2016 11:49 PM, Donovan Parks wrote:
What menu did you put this under? It could probably go under the "power" menu as it isn't going to be of interest outside of developers.
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I do find this pretty confusing. I think it would be best if it was its own command (i.e., gtdb metadata genome_paths or gtdb power genome_paths).
The new command ( gtdb power genome_paths) has been implemented and will be released in the next GTDB version