[Bioperl-l] GenBank XML format?

Chris Fields cjfields at illinois.edu
Wed Jan 28 19:22:24 UTC 2009

We have a module in Bugzilla that hasn't been tested yet:


It needs tests prior to incorporating into core.


On Jan 28, 2009, at 1:13 PM, Dan Bolser wrote:

> Hi,
> Can BioPerl handle GenBank XML format? How about the various 'native'
> database XML formats? Should I just fall back on GenBank text format
> for the given division?
> To be clear I'm thinking about parsing dbEST data. The following
> 'queries' highlight the different formats:
> # A 'native' ASN.1 format dbEST record
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native
> # A 'native' XML format dbEST record
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucess&id=116038450&rettype=native&retmode=xml
> # GenBank text format dbEST record:
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=text
> # GenBank XML format dbEST record:
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&id=116038450&rettype=gb&retmode=xml
> (If any of the above 'queries' fail (Bad Gateway, or anything else
> weird), just try again in a couple of seconds).
> Note that setting db=nucleotide has no effect over setting db=nucess,
> so I guess I may as well use the BioPerl GenBank parser. The reason I
> ask is because I have had trouble using XSLT on large documents, and I
> wondered if BioPerl used some tricks to get round this (if it can read
> these XML formats).
> Thanks for any suggestions,
> Dan.
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