[Bioperl-l] retrieve refseq ids from UIDs

[Smithies, Russell]

Gene and tax data are all tab-separated so it's just a matter of splitting into a hash then querying.
There's a readme in each file (I think) that describes what goes where.

--Russell

> -----Original Message-----
> From: carandraug at gmail.com [mailto:carandraug at gmail.com] On Behalf Of
> Carnë Draug
> Sent: Wednesday, 29 June 2011 9:24 a.m.
> To: Smithies, Russell
> Cc: bioperl mailing list
> Subject: Re: [Bioperl-l] retrieve refseq ids from UIDs
> 
> 2011/6/28 Smithies, Russell <Russell.Smithies at agresearch.co.nz>:
> > It's fairly common for NCBI to return partial or incomplete data,
> often 1/2 a record is missing or requests will time-out at random.
> > If you have a lot of records, it may be better to download all the
> data from the ftp site then parse it locally. This is what we tend to
> do if there's more than a few hundred queries. I'd like to point out
> that it's NCBIs problem, not the BioPerl code at fault. You'll run into
> the same problems if you use NCBIs Perl API
> (http://www.ncbi.nlm.nih.gov/books/NBK1058/) directly.
> 
> Is there any way to catch this kind of errors? Other than repeat
> fetching the data until there's two consecutive results that have the
> same result?
> 
> > Take a look at the gene2accession, gene2refseq, and gene_info data at
> ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ and at the tax data
> ftp://ftp.ncbi.nih.gov/pub/taxonomy/ if you need to decode the taxids
> without doing web queries.
> > It's much easier/faster to download these files, index them, them
> search rather than do queries against NCBI.
> 
> Any module already done written to parse these guys?
> 
> Thanks for all your answers,
> Carnë
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