Driving NCBI BLAST from python without writing to disk

blast-pipe.py

import os
from Bio.Blast.Applications import NcbiblastpCommandline
from Bio import SeqIO


# Grab any sequence to blast
with open("db.fasta", "r") as f:
    record = next(SeqIO.parse(f, "fasta"))

read, write = os.pipe()
parent = os.fork()

if parent:
    os.close(write)
    read = os.fdopen(read)
    cline = NcbiblastpCommandline(db="db.fasta")
    cline(stdin=read.read())
    exit()

else:
    os.close(read)
    write = os.fdopen(write, "w")
    SeqIO.write(record, write, "fasta")
    write.close()
    exit()