cgeb2001's DokuWiki!

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**Quick taxonomy recovery** using the Accession numbers from either a Blast or Plast output:\\

use acc2tax program available in the environmental path.\\

here is an example of how to run it for protein IDs (-p):\\

acc2tax -i /db1/extra-data-sets/Acc2tax/acc2taxIN_example -p -d /db1/extra-data-sets/Acc2tax/Acc2Tax_071119 -o taxonomy.out

don't forget to make sure that your input file contains only the accession numbers without their version, see the example file given above.

-_- E.g., MBI4782295.1 shall be MBI4782295, otherwise the bugs will occur:

<code>
Couldn't find: [MBI4782295.1]

</code>

'^_^' Trim the version ".1" behind the accession MBI4782295.1

<code>
> sed 's/\(.*\)\..*/\1/g' file >out_file

</code>

Note: It still could acquire a lot of unknown even the NCBI taxonomy database is the latest. Any ideas?

==========================
acc2tax database:\\

/scratch3/rogerlab_databases/other_dbs/Acc2Tax_Feb122021		(Up to date Feb 23, 2021)

/misc/db1/extra-data-sets/Acc2tax/Acc2tax_092021		(Up to date Sep 20, 2021)
\\

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