Bioperl: Bio::Index examples bug?

[James Gilbert]

Hi Mark,

Thanks for pointing this out.  The mistake was
actually in Bio::Index::Abstract, where we shold
have doen upcast to Bio::Index::Fasta before
performing the version checks.  bpfetch.pl was
also slightly out of step with the release.

I've fixed this in the bioperl-0.6 branch and in
the main trunk, and made sure that the tests will
catch this in future.  (The changes won't be
immediately visible on the public sites.)

	James

> I haven't played with the Bio::Index modules much, but they look perfect for a
> task at hand.  I believe I have found a bug in the examples released with
> BioPerl 0.6, however.
> 
> scripts/bpindex.pl - works as advertised.
> 
> scripts/bpfetch.pl - has a problem.
> 
> Everytime I call bpfetch.pl on an index created by bpindex.pl, it fails long
> before it ever tries to access the DBM file. It seems that for "local" indexes,
> it first checks its "type_and_version" which calls "_version" to check that the
> versions match. So far, quite nice, however, in bpfetch.pl, it does a clever
> trick of calling Bio::Index::Abstract->new() to open the DBM index file and then
> having the index object re-blessed into the correct type.  The problem is that
> Bio::Index::Abstract->_version() throws an error, claiming that the method must
> be declared by the sub-type. Unless, I badly misunderstand what is going on
> here, I think bpfetch.pl is broken.
> 
> Since I needed a Fasta Index anyway, I merely replaced
> Bio::Index::Abtract->new() with Bio::Index::Fasta->new() and things worked well.
> 
> SUMMARY: It appears to me that the example, bpfetch.pl, is out of date with the
> current (and apparently good) version of Bio::Index::Abstract.  I might be able
> to make changes to bpfetch.pl, but the original author has done a very pretty
> job of coding things so before I try and submit fixes, I'll mention the bug and
> perhaps the author can find a pretty solution for fixing them.
> 
> Thanks to all the authors for a very useful set of modules!
> 
> Mark
> 
> --
> Mark Dalphin                          email: mdalphin@amgen.com
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> 
> 
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James G.R. Gilbert
The Sanger Centre
Wellcome Trust Genome Campus
Hinxton
Cambridge                        Tel: 01223 494906
CB10 1SA                         Fax: 01223 494919

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