[Bioperl-l] TIGR parser for SeqIO

[Josh Lauricha]

On Fri 11/12/04 16:05, Ed Robinson wrote:
> I am trying to get the tigr parser to work on our files.  My
> script is otherwise ok, because when I call a genbank file
> with the genbank parser, I am able to load data.  I have
> downloaded the most recent tigr.pm from the CVS.  When I run
> it, I get this:
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: [46]Required <EXON> missing

Could you privately e-mail me lines around 46 from your input file (10
before, 10 after should be enough) or give me a URL to your file.

> When I use the tigr.pm that comes with the bioperl release we
> have installed, I get the following:
<snip>
> Died at /usr/lib/perl5/site_perl/5.6.1//Bio/SeqIO/tigrxml.pm
> line 150.
>  at
> /usr/lib/perl5/site_perl/5.6.1/i386-linux//XML/LibXML/SAX.pm
> line 63


The "tigrxml" module is not for FULL TIGR files. It is for the tigr
coordset files. The tigr.pm module is for the full TIGR files.

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