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fhcrc / taxtastic

Create and maintain phylogenetic "reference packages" of biological sequences.
GNU General Public License v3.0
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evaluate leaving no_rank taxa in database and expanding on the fly #99

Closed nhoffman closed 6 years ago

nhoffman commented 7 years ago

Expanding the no_rank taxa (see taxtastic.ncbi.db_load() and taxtastic.ncbi.adjust_node_ranks()) may be better done on the fly when requesting lineages, and it may also be useful to retrieve the native ncbi representation. It also takes a while to do this when loading the database. As a starting point, let's add an argument db_load(expand_ranks=True) with a corresponding command line option to set expand_ranks to False. The only tricky part here will be to determine an ordering of the ranks. See https://github.com/fhcrc/taxtastic/blob/master/taxtastic/ncbi.py#L262

crosenth commented 7 years ago

What is the pplacer requirement for expanded no_rank taxa?

nhoffman commented 6 years ago

done in 0.8.1