Seq retrieval tool Announce

[Peter Rice]

David Bauer wrote:
> this is a nice remote entrez client.
> But why don't you use the url method to retrieve entries from ncbi and
> embl?

True, but ...

The EMBOSS url method has already needed C source code changes when Entrez
output (and SRS output) changed. It can be very useful to have a script to
process these sites.

It is also a great help to have a script like this as a model for how to
use the external application access method.

The original external application was the ACEDB 'efetch' utility, no longer
needed because EMBOSS now uses (and creates) 'efetch' index files to index
databases.

You can also use GCG's typedata as an external application, to save
reindexing a GCG database.

External applications normally read one entry at a time, but if gbwget can
read more than one entry and return them in an EMBOSS-friendly format then
it will do something URL access does not.

It could also produce more helpful error messages when access fails.

Peter

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Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723