[Bioperl-l] SeqIO::GeneConstructionKit ??

[Cook, Malcolm]

Thanks for the directions Jason,

I've written SeqIO parsers before for other formats (i.e. DNAStar / Lasergene) and scripted SeqIO allot.

But GCK has a binary format that I was hoping not to have to crack if it had already been done.


Regards,

Malcolm



> -----Original Message-----
> From: Jason Stajich [mailto:jason at cgt.duhs.duke.edu]
> Sent: Tuesday, September 16, 2003 12:43 PM
> To: Cook, Malcolm
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] SeqIO::GeneConstructionKit ??
> 
> 
> I'm not really familiar with the format but in principal if 
> you write a
> SeqIO parser for GCK then it is trivial to do the conversion. 
>  Depending
> on how much information you are trying to save from the 
> conversion - just
> the sequence data or presumably the annotation data as 
> well...  Look at
> SeqIO/genbank.pm and SeqIO/embl.pm the next_seq method to see 
> how we build
> a sequence object up from the parsed data.
> 
>