[Bioperl-l] Usage of tigr.pm with SeqIO.pm

[Simon K. Chan]

Hi BioPerl-ers,

I would like to know if anyone out there has had success in using the SeqIO
module to convert a TIGR xml file to Genbank/fasta/etc or to go the other way
around (ie Genbank to TIGR xml).  

At the moment, converting a TIGR XML file to a genbank file *appears* to work
ok, although I get a large number of error messages:

Use of uninitialized value in numeric lt (<) at
/home/skchan/bioperl/bioperl-live/Bio/PrimarySeq.pm line 355.


Currently, tigr.pm cannot handle all of the tags in the TIGR XML DTD.  A past
member of the lab has added methods to handle the "missing" tags. For example,
the _process_tiling_path method has been implemented in this version
(see http://bioperl.org/pipermail/bioperl-l/2004-February/015004.html )

I have inherited this code and intend to hack in the ability to import/export
TIGR XML format in a reliable fashion.

Any pointers, comments, ideas, and yes, even flames!, would be much appreicated.
:-)

Many thanks, All.


-- 
Warmest Regards,
Simon K. Chan
Bioinformatics, Crosby Lab
skchan at cs.usask.ca