[Bioperl-l] Bio::DB:GFF queries

[Eric Snyder]

Dear BioPerl folks,

I am trying to make use of Bio::DB:GFF for the first time.  I have a mySQL database with the test dataset (used in validating the bioperl install) and am trying to use some of the example code from the synopsis from that module.  I am having some specific problems getting this to work, plus some general questions about how features are named and the impact this has on using the built-in queries.

First, the general questions:

If I understand the GFF spec properly, it can support features of any name.  In the case of the data I am working with, I have sequences with the following features: "First", "Internal", "Initial", "Terminal", "Single".  These all refer to types of exons.   However, I don't see any reason why Bio::DB:GFF should know that.  Consequently then, are the methods for retrieving exon and intron sequences useless to me?  In other words, there appear to be some (undocumented?) assumptions about how features are named in the GFF files that I need to know so I can format my data appropriately so that the GFF module can do the right thing.

If this is true, are these requirements written up somewhere?  As a user, does it make sense for me change my data to fit the module?  Or might certain logical leaps work... For instance, since my data does not contain the "exon" feature but rather, say, the "Internal" feature, would something like $seg->Internal work?  I have not been able to make it work and I fear wishful thinking coupled with ignorance of the details of the implementation of the modules.

Comments, pointers, suggestions?

Also, WRT the mailing list, when I tried to renew my subscription to this list, the web page told me that I was already subscribed.  However, I haven't been receiving emails from this lists since I canceled out of it about 6 months ago.   I just want to make sure that I see the follow-ups to this query.

Many thanks,



Eric E. Snyder
Associate Professor
Pennington Biomedical Research Center
6400 Perkins Road
Baton Rouge, LA 70808-4124
USA
Phone:  (225) 763-3185
Fax: (225) 763-2525
Email: eesnyder@pbrc.edu 
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