[Bioperl-l] Getting errors parsing TIGR XML in SeqIO

Jason Stajich jason at bioperl.org
Tue Jun 30 01:03:08 EDT 2009


There are several flavors of TIGR XML for rice and arabidoposis, and  
other projects etc, I don't know which is tracked with the current  
tigrxml version unfortunately but one can compare the test files in t/ 
data to the versions downloaded to see what is currently supported.   
Usually the gbk will be more consistently parseable but we can try and  
work it out if it is a sensible transformation.

On Jun 26, 2009, at 2:55 AM, Moore, Jonathan wrote:

> I'm trying to parse the TAIR9 Arabidopsis release from the TIGR XML  
> files at the TAIR FTP site.
>
> I've tried SeqIO with both tigr and tigrxml formats but both are  
> giving errors in 1.6.0.  Has anyone advice on whether it's likely to  
> be doable, or should I wait til the .gb files are available?
>
> Jay Moore
>
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--
Jason Stajich
jason at bioperl.org






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