Trouble with blastp against a local database (BioPython)

Question

[alissamariewilliams2015]

I've been having a ton of trouble trying to blastp my file of four protein sequences against a local database of protein sequences. I've been working on this for three days now using the BioPython manual and several fixes I found on the internet, but nothing has worked for me. My issue is that the command runs, but no results file is created.

Currently, this is what I have:

from Bio import SeqIO
from Bio.Blast.Applications import NcbiblastpCommandline

blast_handle = NcbiblastpCommandline(query='PATH/to/genes_of_interest.fasta', db='/PATH/to/local/db/protein.fa', out='PATH/to/results.xml')

When I print blast_handle, I get this:

blastp -out /PATH/to/results.xml -query /PATH/to/genes_of_interest.fasta -db /PATH/to/local/db/protein.fa

However, when I go to /PATH/to/, results.xml is nowhere to be found.

Any help would be much appreciated!

[Pierre Lindenbaum]

check your PATH http://www.linfo.org/path_env_var.html

[alissamariewilliams2015]

I changed it last week (in my .bash_profile), plus wouldn't it give me an error if it couldn't find the PATH? instead of running the command and just not making an output file

[GenoMax]

Have you verified your blastp install and made sure the command is working outside of biopython?

[alissamariewilliams2015]

Yes, blastp works fine outside of BioPython; I changed the PATH in my .bash_profile and tested it out last week.

Answer 1

[alissamariewilliams2015]

I figured it out! After the NcbiblastpCommandline() function, you need to have:

stdout, stderr = blast_handle()

hopefully this will help someone else! Thanks for the replies!