Bioperl: Feature mapping.. clone to contig and vice versa

[shivakd@slip.net]

At 02:08 PM 3/24/00 -0500, Doug Hyatt wrote:
>
>Hello,
>
>I am looking for a script or routine that maps
>feature coordinates (i.e. of genes, exons, repeats, etc.)
>from their positions in a clone to the corresponding
>positions in the contig and vice versa (from contig to
>clone).   
>
>Has such a routine been written for BioPerl?  If 
>not, I will be writing one... is there interest in
>this?

I've used Boulder::Genbank to do something similar in the past (this
assumes of 
course you are parsing Genbank records to get the tags).  Boulder::Genbank
will get the tags by range, which you can then offset for the contig
position.  I'm sure there is the same functionality in BioPerl but I am
haven't explored it yet.

E.g... from the Boulder::Genbank page:
my @features = $data->features(-type=>[ qw(Exon Source Satellite) ], 
                                      -pos=>[90,310] );
       foreach (@features) {
          print $_->Type,"\n";
          print $_->Position,"\n";
          print $_->Gene,"\n";

Dave

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