cgeb2001's DokuWiki!

You've loaded an old revision of the document! If you save it, you will create a new version with this data.

**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>

:-D Trim the version ".1" behind the accession MBI4782295.1

<code>
> cat file | cut -d '.' -f1 > out_file

</code>

Note: 
1. You can get the accession list from Blast/Plast result (output.txt) directly using the command below:

<code>
> cat output.txt | cut  -f2 | cut -d '.' -f1 > out_file
</code>

2. If there are "|" in the accession numbers (i.e., gb|KAA8922376.1|)

<code>
> cat output.txt | cut -d "|" -f2 | cut -d '.' -f1 > out_file
</code>

3. It can still acquire a list of unknown like below even the NCBI taxonomy database is updated to the latest.

<code>
Couldn't find: [MBR3349819]
Couldn't find: [HBS54143]
Couldn't find: [MYJ28876]
</code>

This might due to these protein IDs(MBR3349819,HBS54143) from the species cannot put into the taxonomy like NP_051083. i.e., Lineage is not in (full) status.

<code>
NP_051083	cellular organisms,Eukaryota,Viridiplantae,Streptophyta,Streptophytina,Embryophyta,Tracheophyta,Euphyllophyta,Spermatophyta,Magnoliopsida,Mesangiospermae,eudicotyledons,Gunneridae,Pentapetalae,rosids,malvids,Brassicales,Brassicaceae,Camelineae,Arabidopsis,Arabidopsis thaliana
</code>

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

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

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

/scratch3/rogerlab_databases/other_dbs/Acc2Tax_Jan2022		(Up to date Jan 30, 2022, wgs not included in nucl_all.txt)
\\

Please fill all the letters into the box to prove you're human. W G K C E Please keep this field empty:

Edit summary

Note: By editing this page you agree to license your content under the following license: CC Attribution-Noncommercial-Share Alike 4.0 International