Parsing Description from NCBI Blast+

Question

[onspotproductions]

I used BLAST plus to Blast an assembly against a uniprot database, and want to parse the description of the uniprot ID from the uniprot database I am comparing the fasta file to.

[5heikki]

How is your blast output file? Is it tabular (-outfmt 6)? What is the uniprot id-description map file like? Post a few example lines please..

[onspotproductions]

blastx -db UniprotConus -query /Users/***/Desktop/Cone_Snail_Assembly.txt -outfmt "10 qseqid sallseqid sscinames scomnames sblastnames pident length mismatch gapopen qstart qend sstart send evalue bitscore sseq qseq" -out UniprotConusBLASTFull2.txt

The uniprot is simply a fasta file made into a database using makeblastdb. lines like this e.g.

>sp|P86500|CX21A_CONPU Conotoxin p21a OS=Conus purpurascens PE=1 SV=1
FELLPSQDRSCCIQKTLECLENYPGQASQRAHYCQQDATTNCPDTYYFGCCPGYATCMSI
NAGNNVRSAFDKCINRLCFDPGH

Answer 1

[dschika]

Use grep or e.g. python dictionaries. You may also specify your question...