[Biopython] How to run esearch in BioPython without specifying any filtering terms

[bar tomas]

Thanks a lot. I understand now.

On Wed, Jul 15, 2009 at 9:16 PM, Brad Chapman <chapmanb at 50mail.com> wrote:

> Hello;
>
> > The BioPython tutorial (p.86) shows how once the available fields of an
> > Entrez database have been found with Einfo ,  queries can be run that use
> > those fields in the term argument of Esearch (for instance Jones[AUTH]).
> >
> > However, I?d like to retrieve all IDs from a database without specifying
> any
> > filtering term.
> >
> > If I leave the term argument out in the Entrez.efetch method, BioPython
> > returns an error.
> [..]
> > How can you run esearch in BioPython with no filtering terms?
>
> Retrieving all IDs isn't practical for most of the databases due to
> large numbers of entries. That's why a term is required in Biopython,
> and why most NCBI databases likely won't have an option to return
> everything. For example, 'pcsubstance' looks to contain 81 million
> records from the available downloads:
>
> ftp://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/XML/
>
> To realistically loop over a query, you'll need to limit your search
> via some subset of things you are interested in to make the numbers
> more manageable.
>
> Hope this helps,
> Brad
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