[Biopython] Piping in and out of clustal
Ivan Gregoretti
ivangreg at gmail.com
Thu Mar 28 15:26:05 UTC 2013
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
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