'blastp' is not recognized as an internal or external command error when running blast with python

I'm trying to run a local BLAST with biopython using Bio.Blast.Applications. However, when running the below code:

from Bio.Blast.Applications import NcbiblastpCommandline

result = r"C:\Users\Uzytkownik\Desktop\tests\result.xml" 
q = r"C:\Users\Uzytkownik\Desktop\tests\fastas\my_example2.faa"
database = r"C:\Users\Uzytkownik\Desktop\tests\my_examplemultif.faa"

blastp_cline = NcbiblastpCommandline(query = q, db = database, evalue = 0.001, outfmt=5, out = result)
stdout, stderr = blastp_cline()

I receive an error stating:

ApplicationError: Non-zero return code 1 from 'blastp -out C:\\Users\\Uzytkownik\\Desktop\\tests\\result.xml -outfmt 5 -query C:\\Users\\Uzytkownik\\Desktop\\tests\\fastas\\my_example2.faa -db C:\\Users\\Uzytkownik\\Desktop\\tests\\my_examplemultif.faa -evalue 0.001', message "'blastp' is not recognized as an internal or external command,"

I've tried running this with subprocess and os., but got the same error every time.

When I run the query through the command line everything works fine (I'm using blast 2.9.0+), so I'm really not sure what the issue is. Would be gratefull for any help!

Solution

First find the location where your blastp executble is installed and give that as argument to NcbiblastpCommandline.

from Bio.Blast.Applications import NcbiblastpCommandline

blastp_path = r"C:\path\to\blastp.exe"
result = r"C:\Users\Uzytkownik\Desktop\tests\result.xml" 
q = r"C:\Users\Uzytkownik\Desktop\tests\fastas\my_example2.faa"
database = r"C:\Users\Uzytkownik\Desktop\tests\my_examplemultif.faa"


blastp_cline = NcbiblastpCommandline(cmd=blastp_path, query=q, db=database, evalue=0.001, outfmt=5, out=result)

If you now do print(blastp_cline) it should print out the full command that is going to be run. Doublecheck that this works by copy/pasting this output and running it from the commandline. If that works, then

stdout, stderr = blastp_cline()

should work too.