This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Modifying Standalone BLAST output

I am performing a standalone BLAST in ubuntu, I have downloaded the environmental metagenome (env_nt) database from NCBI. The cmd which I am using to perform BLAST is -> 

blastn -db env_nt -query file.fasta -out BLAST_output.fasta -max_target_seqs 1 -outfmt '6 qseqid qseq sallseqid stitle score bitscore qcovs evalue pident sacc staxids sscinames scomnames sblastnames'

But in this output I also need the organisms name or the source name of the subject hit which I am obtaining form the BLAST. Can anyone help me regarding this? What syntax should I use to obtain the organism/source name? Thanking you.

blast
• 2,790 views • link
updated by 5heikki 5heikki • written by glady glady

can you provide several lines of the result?

• 0 views • link
written by shenwei356 shenwei356

2 answers

I tried before but failed. These's an indirect way.

ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz provides mapping relationship between accessions (sseqid) and taxid, which you can use to get the organisms name.

dummy data

$ cat t.tsv 
P05876  other-info
P27125  other-columns

get accession

$ cut -f 1 t.tsv > t.acc

get taxid

$ csvtk grep -t -f 1 -P t.acc prot.accession2taxid.gz | cut -f 1,3 | sed 1d > t.acc2taxid

get lineage

$ cat t.acc2taxid |  taxonkit lineage -i 2 > t.acc2taxid.lineage

merge taxid and lineage back to the blast result

$ csvtk join -H -t t.tsv t.acc2taxid.lineage
P05876  other-info      11731   Viruses;Retro-transcribing viruses;Retroviridae;Orthoretrovirinae;Lentivirus;Primate lentivirus group;Simian immunodeficiency virus;Simian immunodeficiency virus - agm;Simian immunodeficiency virus - agm.ver;Simian immunodeficiency virus (TYO-1 ISOLATE)
P27125  other-columns   83333   cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12

you may need csvtk and taxonkit.

• 0 views • link
written by shenwei356 shenwei356

You have to setup taxdb but with env_nt I think all the sequences are basically annotated as "Environmental sample" so not much will be gained..

• 0 views • link
written by 5heikki 5heikki

Log in to answer this question.

More posts like this