cgeb2001's DokuWiki!

This is an old revision of the document!

---

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:

Couldn't find: [MBI4782295.1]

Trim the version “.1” behind the accession MBI4782295.1

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

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

Couldn't find: [MBR3349819]
Couldn't find: [HBS54143]
Couldn't find: [MYJ28876]

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.

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