incertae sedis erroneouly retained in synthetic tree

OpenTreeOfLife / treemachine

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incertae sedis erroneouly retained in synthetic tree #168

Closed jar398 closed 9 years ago

jar398 commented 9 years ago

The current synthetic tree shows OTT taxon 5268476, which is an incertae_sedis container:

https://tree.opentreeoflife.org/opentree/otol.draft.22@384700/Incertae-Sedis

It's a bug that it didn't get squeezed out when OTT 2.8 was generated, but I thought that it would be suppressed by treemachine on load. Here's the row from OTT:

and here's the code from GraphInitializer.java:

        if (tflag.equals("incertae_sedis")){
            System.out.println("skipping incertae_sedis "+name);    
            return;
        }

so I'm baffled as to how this could happen.

josephwb commented 9 years ago

Treemachine only uses the flags to determine whether a taxon should be pruned. The version we were using (2.8draft5) has the following:

grep "^5268476" Filtered_OTT_taxonomy.tsv
5268476 |   304358  |   Incertae Sedis  |   no rank |   silva:L37037/#2 |   Incertae Sedis (in domain Eukaryota)    |       |

So, no flag. I don't think treemachine made an error here, so I am closing the issue.

jar398 commented 9 years ago

OK, I was looking at 2.9, which has it flagged. This is unfortunate...

blackrim commented 9 years ago

Yeah. It is in a pretty good sized list of taxonomy things.

josephwb commented 9 years ago

To be clear: no taxa with the "incertae_sedis*" flag is in the tree. JWB.

On 8 April 2015 at 09:08, Stephen Smith notifications@github.com wrote:

Yeah. It is in a pretty good sized list of taxonomy things.

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/treemachine/issues/168#issuecomment-90909704 .