[Bioperl-l] Constructing split features

[Jason Stajich]

Yes you can make your own feature and add it to a Bio::Seq object - the
location is stored in a location object which you can copy and manipulate
or change getter/setter is $feature->location
$feature->location($newlocation)

Some code here to explain more:
http://bioperl.org/wiki/HOWTO:Feature-Annotation#Location_Objects

Where it is unclear, be GREAT for you or others to add more text to the
HowTo as well.

Also, lots of this hard work taken care of when you have the complete
genome in one place, ala Ensembl or UCSC where you can download complete
GFF and CDS & AA already (if you are working with data for species in their
systems) -- but you must have some reason to get it from genbank directly?




Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki/User:Jason
http://twitter.com/hyphaltip


On Fri, Apr 18, 2014 at 11:51 AM, Warren Gallin <wgallin at ualberta.ca> wrote:

> It occurs to me that if one could create a Bio::SeqFeature object using
> the information in a coded_by tag from a CDS Bio::SeqFeature in a protein
> record, then it should be possible to add that new feature to a copy of the
> underlying nucleotide sequence (just pull the sequence from GenBank in fast
> format, create a temporary new GenBank format Bio::Seq object, add the
> single new feature and use it to extract the spliced sequence).
>
> Is this even possible?  Or would you have to strip out all the information
> on the various spliced locations from the coded-by tag and rebuild a new
> Bio::SeqFeature from scratch?  Or is this even a reasonable approach to
> creating an automated way of getting coding sequences?
>
> Warren Gallin
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