Creating a taxon.db database with taxit

[Greg G]

Hi all,

While using Taxit 0.8.5 on my Ubuntu 16.04 computer: I'm getting an error during the taxonomic database creation step (I'm following the Taxit documentation here).

Command: taxit new_database -d taxonomy.db

Error: unrecognized arguments: -d

There is an open bug report for this issue on the Taxit Github page, but since it has gone unanswered, I am wondering if anyone here has found a workaround.

Alternately, does anyone know how to output the placements of a Jplace file into tabular format? That's what I'm ultimately trying to achieve.

Best,

Greg

[Erick Matsen]

Hi Greg--

I can't help you with the taxit issue, but re tabular format see

https://matsen.github.io/pplacer/generated_rst/guppy_to_csv.html#guppy-to-csv

Erick

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Frederick "Erick" Matsen, Associate Member
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[Chris Rosenthal]

Hi Greg,

I am in the process of updating the Taxtastic documentation and have responded to the Taxit Github Issue here.  In short, you do not need the -d flag anymore just `taxit new_database taxonomy.db`.  Thank you for your email.

Chris

[Greg G]

Wonderful, thanks!