[Biopython] Piping in and out of clustal

[Ivan Gregoretti]

Hello Biopythonians,

Both Biopython's documentation and common sense agree in that we
should not try to code in Python algorithms that have been already
developed and tested outside Python. That is why Biopython offers very
convenient interfaces to many bioinformatics programmes like Clustal
Omega among them.

In general, this is how I set Clustal up

clustalo_cline = ClustalOmegaCommandline(infile='input.fa', outfile='output.fa')

and this is how I execute it

stdout,stderr = clustalo_cline()

That is fine. Here comes the problem:

I need to run a million times (and in multiple cores) very brief
clustal executions.
Is there a way to pass/get SeqRecords to/from Clustal without the
creation of input and output files?

Or, simply put,

Can I pipe in and out of Clustal from within Python?

Thank you,

Ivan




Ivan Gregoretti, PhD