[Bioperl-l] Re: [Bioperl-guts-l] bioperl commit

[Allen Day]

Chris, what does this mean?  We are using produced_by in many places in
Chado.

-Allen


On Thu, 8 Apr 2004, Chris Mungall wrote:

> 
> cjm
> Thu Apr  8 01:54:03 EDT 2004
> Update of /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Tools
> In directory pub.open-bio.org:/tmp/cvs-serv13283
> 
> Modified Files:
> 	TypeMapper.pm 
> Log Message:
> 
> 
> bioperl-live/Bio/SeqFeature/Tools TypeMapper.pm,1.6,1.7
> ===================================================================
> RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm,v
> retrieving revision 1.6
> retrieving revision 1.7
> diff -u -r1.6 -r1.7
> --- /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm	2004/03/13 01:10:42	1.6
> +++ /home/repository/bioperl/bioperl-live/Bio/SeqFeature/Tools/TypeMapper.pm	2004/04/08 05:54:03	1.7
> @@ -278,9 +278,14 @@
>     my $type = 'part_of'; # default
>  
>     # TODO - do this with metadata, or infer via SO itself
> -   if (lc($child) eq 'protein' or lc($child) eq 'cds') {
> +
> +   if (lc($child) eq 'protein') {
> +       # DEPRECATED!!!
>         $type = 'produced_by';
>     }
> +   if (lc($child) eq 'polypeptide') {
> +       $type = 'derived_from';
> +   }
>     return $type;
>  }
>  
> 
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