Question

it’s the first time that i use blast inside biopython, and i’m having a problem.

i created a custom blast database from a fasta file which contain 20 sequence using :

os.system(‘makeblastdb -in newtest.fasta
-dbtype nucl -out newtest.db’)

and this did generate few files (newtest.db.nhr, newtest.db.nin, newtest.db.nsq) inside the current directory that i’m currently working in : (/home/User/Documents/python/fasta-files)

and now i’m trying to query this database inside biopython using :

blastx_cline = NcbiblastxCommandline(query="queryfile.fas", db="newtest.db", evalue=0.00000001, outfmt=5, out="opuntia.xml")

but i’m getting this error :

> Bio.Application.ApplicationError: Command 'blastx -out opuntia.xml
> -outfmt 5 -query queryfile.fas -db newtest.db -evalue 1e-08' returned non-zero exit status 2, 'BLAST Database error: No alias or
> index file found for protein database [newtest.db] in search path
> [/home/User/Documents/python/fasta-files:/usr/share/ncbi/blastdb:]'

so i tried copying the files generated from the /home/User/Documents/python/fasta-files to /usr/share/ncbi/blastdb but it says that i don’t have permission.

*EDIT*

when i use : os.system("blastn -db newtest.db -query "fastafile.fas" + " -out test.txt")
it works normally generating an output file. but not the other way around**

so i’m stuck here and i don’t know how to solve this.

any help would be appreciated

Answer 1

Pay attention to phrase protein database in the error message while newtest.db is a nucl database.

index file found for protein database [newtest.db] in search path

So blastx is expecting a protein database. Isn’t that obvious? 🙂

In case you did not do it by purpose, you should specify BLAST program to use by adding “cmd=’blastn'”. So, this is better:

blastx_cline = NcbiblastxCommandline(cmd='blastn', query="queryfile.fas", db="newtest.db", evalue=0.00000001, outfmt=5, out="opuntia.xml")