blast with python don't run

Question

[flogin]

Hello guys, I'm studying how run a blast analysis with python, and I found the Bio.Blast.Applications my blast version is: Package: blast 2.6.0, build Jan 15 2017 17:12:27, and I write this code:

import argparse
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio.Blast.Applications import NcbimakeblastdbCommandline

parser = argparse.ArgumentParser()
parser.add_argument("-in", "--input", help="fasta file to use as query",  required=True)
parser.add_argument("-db", "--database", help="fasta file to use as database",required=True)
args = parser.parse_args()
read_file = args.input
database = args.database

clinedb = NcbimakeblastdbCommandline(dbtype="nucl", input_file = database)
clinedb
cline = NcbiblastnCommandline(query = read_file, db =database, out = read_file+'.blastn', outfmt = 6, evalue = 0.001)
cline

When I run python test.py -in genome_1.fasta.fmt.kmers -db genome_2.fasta nothing happens.

If I print the variables clinedb and cline:

makeblastdb -dbtype nucl -in genome_2.fasta 
blastn -out genome_1.fasta.fmt.kmers.blastn -outfmt 6 -query genome_1.fasta.fmt.kmers -db genome_2.fasta -evalue 0.001

How can I solve this?

Answer 1

[gb]

have you tried:

stdout, stderr = cline()

[flogin]

It's works, thanks gb, I'm gonna study this structure 'stdout, stderr = cline()'.

[gb]

Think this can help to understand it in detail https://biopython.org/DIST/docs/api/Bio.Blast.Applications-pysrc.html https://biopython.org/DIST/docs/api/Bio.Blast.Applications.NcbiblastnCommandline-class.html

[Joe]

stdout, stderr = cline() is capturing the output of the command, else it runs entirely silently.

AFAIK, it should still have generated the output files, just silently, but perhaps there's some quirk that means it wont.