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

Simon K. Chan skchan at cs.usask.ca
Tue Apr 27 17:29:24 EDT 2004

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

More information about the Bioperl-l mailing list