[Biopython] Piping in and out of clustal

[Peter Cock]

On Thu, Mar 28, 2013 at 3:26 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
> 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

Yes, according to the Clustal Omega documentation by default it
writes its results (alignments) to stdout, and if you use '-' as the
input filename and it will read from stdin.
http://www.clustal.org/omega/README

If the data is small, you can probably use strings in memory, e.g.
stdout,stderr = clustalo_cline(stdin)

Peter