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

[Fields, Christopher J]

Ross,

The standard way is to check whether the location object is a SplitLocationI or not, see the following for an example:

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Location_Objects

chris

On Nov 27, 2011, at 2:24 AM, Ross KK Leung wrote:

> 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.
> 
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