[Bioperl-l] Check the location type for a particular gene in a Genbank file

[Ross KK Leung]

Hi all,

To write a script to extract sequence generically for all types of
BioLocation objects, I'd like to know if there is any way to check what
types (e.g. simple or split) are being processed.

Bio::Location::CoordinatePolicyI appears to be doing something similar but
it is more like a post checking step. If I parse the genbank file line by
line, I can certainly check whether the line contains keywords like "join"
but as I'm using something like:

        my @features=grep{$_->primary_tag eq $chkTags[0]}
$seqobj->get_SeqFeatures;                                    
 

        foreach (@features) {

            $pseudo=$_->has_tag('pseudo')?'pseudo':'functional';

            @gene=[];                                                   

I'd appreciate if anybody knows a better integration with the well-developed
bioperl module.

Thanks a lot.