How To Get A Blast Record From Stdout Of Ncbiblastxcommandline

Question

[Wrf]

i am blasting sequences from a fasta file individually since the output will be handled differently depending on the quality of the hit.

currently i have this, which works fine:

blast_handle = Blastx_Command(stdin=seq_record.format("fasta"))

however, this involves writing the output to a temporary xml file and then reading it with NCBIXML.parse(file), which is quite slow.

NCBIXML.read() or parse() expects a file, so as far as i understand, it cannot directly take the standard output.

does anyone know a way to take the stdout from the Blastx_Command and somehow turn that into a BlastRecord?

thanks in advance

Answer 1

[Damian Kao]

I am not sure how exactly you are forming your blast commands. But you can try using popen objects. For example

import os
result = os.popen('my blast command')

result is now a file handle that NCBIXML.parse should be able to read.

A simple example that'll list the current directory in linux:

import os
result = os.popen('ls')
for line in result:
    print line

[Wrf]

thanks DK, with some tweaking, that worked. here was the final command:

result_handle = os.popen("echo ""+seq_record.format("fasta")+"" | "+str(Blastx_Command)) record = NCBIXML.read(result_handle)

Answer 2

[Peter]

No, NCBIXML.read() or parse() expects a handle - not a file. This means if you run BLAST via subprocess (or one of the dreprecated alternatives like os.popen) you can get a handle for BLAST's stdout and parse that directly. There are examples of this in the Biopython Tutorial (for multiple sequence alignment tools at least).

Answer 3

[Wrf]

to answer my own question, someone suggested cStringIO, which was implemented as:

import cStringIO
BlastX_Command = NcbiblastxCommandline (db="nt", query="-", outfmt=5)
blast_handle = cStringIO.StringIO(Blastx_Command(stdin=seq_record.format("fasta"))[0])

for record in NCBIXML.parse(blast_handle):

etc...