[Bioperl-l] fetching exons in genomic coordinates from NCBI

[Chris Fields]

Bio::SeqIO::entrezgene?  This creates a Bio::Seq::RichSeq from Gene XML (though I don't use it myself).

chris

On May 25, 2011, at 2:13 PM, Dave Messina wrote:

> Hi Reece,
> 
> As far as I know, you're doing it the NCBI recommended way, byzantine though
> it may be. Of course I too would be keen to hear of a better approach if
> anyone's got one.
> 
> 
> Dave
> 
> 
> 
> 
> On Sat, May 21, 2011 at 18:37, Reece Hart <reecehart at gmail.com> wrote:
> 
>> Hi-
>> 
>> I'd like to fetch exons for a given RefSeq in genomic coordinates (GRCh37)
>> directly from NCBI. The only path to this data that I'm aware of is a bit
>> painful: esearch for the gene based on RefSeq accession, efetch the gene
>> record as XML, then parse the XML for Gene-commentary_genomic-coords.
>> That's
>> doable, but unattractive. Anyone got a better way?
>> 
>> Normally I'd fetch these with blissful ease from Ensembl, but the point of
>> this exercise is to compare data for a particular transcript against
>> Ensembl.
>> 
>> Thanks,
>> Reece
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