'blastp' is not recognized as an internal or external command using Bio.Blast.Applications
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15 months ago
perstet • 0

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!

biopython blast • 543 views
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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).

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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+

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