How to get the full taxa of predicted hosts

[WUD2018]

Hey developer,

I noted that the Cherry gives hosts of phage sequences. However, it only lists the species names. How can I get the full taxa? Is there any taxa list?

Thanks.

PS: there are two files (virus.csv & prokaryote.csv) in the './database/cherry' file. Which one should I use?

[KennthShang]

Hi,

Thanks for using our tools. the full taxa can be found in the file "prokaryote.csv"

You can also search for it with the ETE3 toolkit: http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html

Best,
Jiayu

[WUD2018]

Thanks Jiayu,

One more suggestion here: you may note that the gtdbtk has updated its database, which has a new taxa name system. Is it possible for you to update phabox and assign the phage-host names in alignment with gtdbtk (such as v2.3 release 214)

[KennthShang]

Good to know.

We will consider to update the gtdbtk in the near future. (I am sorry that we have to catch up ddl recently

If you are in a hurry, you can convert it by yourself. We provided a script to convert the current results from NCBI taxa to GTDB (in the GTDB folder). If there is a table to align GTDB to gtdbtk, it can be done easily.

Or maybe if you want to share this table with us, that will be helpful to write a script for that.

Best,
Jiayu

[WUD2018]

Thanks, Jiayu,

Here is the taxa table (v2.3.0 release 214):

gtdb_taxonomy.txt

[KennthShang]

Hi there,

I am sorry, but it seems the provided taxa table cannot be used to convert RefSeq into GTDB. I found that many of the sequences in the RefSeq taxa cannot find their corresponding taxa in the provided file (missing many accession maps).

However, I suddenly found that my provided scripts in the GTDB folder had some problems in the previous release. I have fixed the problems with a readme file. Hope it can help you to convert the RefSeq into the wanted GTDB. The GTDB taxa are also downloaded from the official website.

Best,
Jiayu