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!
check your PATH http://www.linfo.org/path_env_var.html
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
Have you verified your blastp install and made sure the command is working outside of biopython?
Yes, blastp works fine outside of BioPython; I changed the PATH in my .bash_profile and tested it out last week.