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

Fields, Christopher J cjfields at illinois.edu
Mon Nov 28 14:42:12 EST 2011


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



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.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list