[Biopython-dev] [Bug 2652] Bio.Fasta.Iterator fails with IndexError when opening empty fasta files

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2652





------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2008-11-11 10:28 EST -------
(In reply to comment #2)
> I am using the Biopython package from the debian-lenny repository (which is
> 1.45), I guess they haven't updated in part due to the change to the Numpy. I
> will checkout the svn version then.

Debian sid is using Biopython 1.47, I think lenny is just very conservative.

If you don't mind installing NumPy and trying to install Biopython from source,
then you could either try getting the latest Biopython code from CVS, or try
Biopython 1.49 beta which was released just a few days ago.  Ask on the mailing
list if you get stuck.

> As for why I'm using Bio.Fasta, I'm not using it directly.
> Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.cai_for_gene() calls it.

Oh - thanks for that.  I've just updated Bio/SeqUtils/CodonUsage.py to use
Bio.SeqIO instead of Bio.Fasta (plus added a basic check of this module to our
unit tests).

Peter

[Leaving this bug as resolved fixed]


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