'blastp' is not recognized as an internal or external command using Bio.Blast.Applications

Question

[perstet]

Hello!

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,"

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!

[GenoMax]

blastp is not available in your PATH. Since this appears to be windows you will need to amend PATH accordingly (or provide full path to the blastp executable).

[flogin]

idk if it can help, when I run blast inside python, I put (example with blastx):

from Bio.Blast.Applications import NcbiblastxCommandline

cline = NcbiblastxCommandline(query = query_file, db = database_file, out = query_file+'.blastx', 
outfmt = 6, word_size = 3, evalue = 0.00001, num_threads = threads)
stdout, stderr = clone()

my blast version: Translated Query-Protein Subject BLAST 2.9.0+

Answer 1

[John]

Follow this BLAST+ to install BLAST+ on windows and adding it to the path should work.

from Bio.Blast.Applications import NcbiblastnCommandline

blastn = "C:/path_to_blast/blast-BLAST_VERSION+/bin/blastn"

cline = NcbiblastnCommandline(cmd = blastn,query='query.fasta', out='out.tab', outfmt=6, subject='subject.fasta') stdout, stderr = cline()

print("STDOUT: %s" % stdout)

print("STDERR: %s" % stderr)