omamer mapping to custom database

[xiaoyezao]

Hi omamer designer,

The current omamer use pre-built databases. Is it possible to use custom OrthoXML files generated by OMA standalone?

Thank you,

Tao

[alex-wave]

Hi Tao,

Thank you very much for your question. Recently we have been overhauling the underlying code for the search phase.

Currently it is not possible to build an OMAmer database using OMA standalone results, but we have a plan for how to enable this in the near-future.

I will update this issue when we have made progress.

Thanks,
Alex

[alex-wave]

Hi Tao,

The most recent commit (add1772) on the development branch contains version 2.0.4.dev6.

This version enables building custom databases using custom HOGs in OrthoXML format + sequences in FASTA format + species tree in Newick format. Documentation will be updated after further testing and merging with the main branch.

For an OMA Standalone run, we've tested building a database using the command

omamer mkdb --db standalone.h5 --log_level debug --orthoxml Output/HierarchicalGroups.orthoxml --sequences DB/*.fa --species_tree <path to species tree given to build HOGs>

Please let us know if there are any problems that come up when testing.

Thanks,
Alex