Is there a possibility, using biopython to save output table of blastn in memory, not in file on hard drive, for process it using pandas for example and then delete it from memory?

I mean, is there a possibility to redirect output of "out" argument of this function into memory? In pandas DataFrame for example.

NcbiblastnCommandline(query="fasta1.fasta", subject="fasta2.fasta", out="output_table.csv", outfmt=6)

I always saved output tables in file before, but now I need to align one set of small fasta files against another set of small fasta files and I think that the best way is avoid writing of many small tables in hard drive because after recieving one table I have to read and process this table immediately and after that I don't need this table anymore.


1 Answer 1


You can specify send to stdout using out='-' in the Biopython wrapper.

from Bio.Blast.Applications import NcbiblastnCommandline
import pandas as pd

cline = NcbiblastnCommandline(query='seq.fna', subject='seq2.fna', outfmt=6, out='-')
output = cline()[0].strip()

rows = [line.split() for line in output.splitlines()]
cols = ['qseqid', 'sseqid', 'pident', 'length',
        'mismatch', 'gapopen', 'qstart', 'qend',
        'sstart', 'send', 'evalue', 'bitscore']

data_types = {'pident': float, 'length': int, 'mismatch': int,
              'gapopen': int, 'qstart': int, 'qend': int,
              'sstart': int, 'send': int, 'evalue': float,
              'bitscore': float}

df = pd.DataFrame(rows, columns=cols).astype(data_types)

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