[Biopython] Unix pipes and APIs like NcbiblastxCommandline()

[Ivan Gregoretti]

Hello everybody

Can somebody suggest a way to run an API like NcbiblastxCommandline()
but directing the output to standard output?

For instance, this is the conventional execution with output directed
to a file, in this case opuntia.csv:

from Bio.Blast.Applications import NcbiblastxCommandline
blastx_cline = NcbiblastxCommandline("/mnt/shared/ncbi-blast-2.2.29+/blastx",
query="opuntia.fasta", db="nr", evalue=0.001, outfmt=10,
out="opuntia.csv")

Now, what I would like to know is how to run this API with something like

out="/dev/stdout" instead of out="opuntia.csv".

In other words, I seek to avoid the creation of opuntia.csv.

Optional context:

I can currently execute local blast from within Python and direct its
output to a pipe (i.e. subprocess.Popen...). I am now interested in
trying the API way as it is likely to be more robust than my
implementation and already tested by a very large number of users.

Thank you,

Ivan



Ivan Gregoretti, PhD
Bioinformatics