[Bioperl-l] Bio::Tools::GFF

Chris Fields cjfields at uiuc.edu
Fri Apr 28 09:03:36 EDT 2006


Lincoln's working on GFF3 integration into BioPerl at the moment  
which will not use Bio::DB::GFF, so there's a bit of reluctance at  
the moment to commit this unless Lincoln signals that it's fine.

http://article.gmane.org/gmane.comp.lang.perl.bio.general/10691/match=

http://www.bioperl.org/wiki/ListSummary:April_12-25%2C2006#Bioperl- 
guts_.28for_the_die-hards.29

If you look in CVS in Bio::DB, several new modules have been added  
(also in the ListSummary above).  You could try those out but I have  
no idea what kind of working condition they are in and how stable the  
API is at the moment.

You could email the GMOD lists as well (I get the GBrowse, which  
Scott Cain and Lincoln regularly post to).  Info here:

https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

Chris

On Apr 28, 2006, at 5:41 AM, Paul Mooney wrote:

> Hi,
>
> I've modified one line in my local copy of Bio::Tools::GFF so it takes
> into account *all* of the special tags defined here;
> http://song.sourceforge.net/gff3.shtml
>
> Current CVS version;
> $tag= lcfirst($tag) unless ($tag =~/^ID|Name|Alias|Parent|Gap|Target 
> $/);
>
> My version;
> $tag= lcfirst($tag) unless ($tag
> =~/
> ^ID|Name|Alias|Parent|Gap|Target|Derives_from|Note|Dbxref| 
> Ontology_term$
> /);
>
> Could someone update cvs please?
> Paul.
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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