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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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133 new ranks #137

Closed crosenth closed 4 years ago

crosenth commented 4 years ago

@nhoffman @dhoogest - In addition to Dan's new rank additions I added support for a new rank "clade" that behaves like "no rank". Like "no rank", a "clade" can appear in any rank order and can loop (be a child and parent of itself). A node of rank "clade" will have its rank represented as an underscore prepended to its parent rank.

Example taxtable: taxit taxtable --tax-ids 572265 1228987 1149873 191675

dhoogest commented 4 years ago

@nhoffman @dhoogest - In addition to Dan's new rank additions I added support for a new rank "clade" that behaves like "no rank". Like "no rank", a "clade" can appear in any rank order and is cyclical (can be a child and parent of itself). A node of rank "clade" will have its rank represented as an underscore prepended to its parent rank.

Example taxtable: taxit taxtable --tax-ids 572265 1228987 1149873 191675

Good solution!

crosenth commented 4 years ago

I found another loop in a different rank and decided to do a full count of rank loops:

Screenshot from 2020-07-01 21-55-42

So my solution will not work..

crosenth commented 4 years ago

I think the simplest solution is to treat the 6 rank loops in the exact same way as we've been handling no_rank

crosenth commented 4 years ago

Okay I have a candidate release here. @dhoogest @nhoffman - I created a group of ranks called RANKLOOPS which all get the same parent rank + '' treatment . As far as the new ranks that are not "loop ranks" I could not determine a rank order as none occur together in a single lineage and are all children of rank species at their lowest rank.