[Bioperl-l] Bio::SeqIO::bsml.pm

[Charles Tilford]

All the legal paperwork has finally come in, so I have committed to
bioperl-live the SeqIO module for converting bioseq objects to and
from BSML XML files. It's under SeqIO::bsml.pm.

The module will break with the new Annotation::Collection system,
which is not 100% backwards compatible - the problems I've encountered
are:

* description crashes if there is no description entry present and a
->value call is made on undef

* Annotation.pm would accept an array of references and would add them
all, the Collection will just add the first one

* Annotation.pm would allow empty arguments to be passed (for example,
an empty array to add_Reference, which would then do nothing), whereas
Collection will throw that it expects to see an object at
add_Annotation.

Ewan, do you mind if I make modifications to the backwards-compatible
methods in Collection.pm to address these? I am uncertain how tolerant
you wanted the new module to be.

I will make changes in the next few days to bring bsml.pm into full
compliance with the new Collection system, but in the meantime the 1.1
revision can be used by anyone with the older Annotation.pm.

If you want to view BSML files graphically, free viewing software is
available at:

http://www.labbook.com/products/standards.asp

Much of the BSML DTD involves graphical formatting; bsml.pm concerns
itself almost exclusively with transfering data, so the direct output
will be somewhat plain.

Let me know of any issues seen with the code...

Thanks,
Charles

-- 
Charles Tilford, Bioinformatics-Applied Genomics
Bristol-Myers Squibb PRI, Hopewell 3A039
P.O. Box 5400, Princeton, NJ 08543-5400, (609) 818-3213
charles.tilford@bms.com