[Biopython] History, Efetch, and returned records limits

[Peter Cock]

On Sat, Apr 14, 2012 at 1:35 PM, Mariam Reyad Rizkallah
<mrrizkalla at gmail.com> wrote:
> Dear community,
>
> I aim to get sequences by a list of gi (using efetch and history
> variables), for a certain taxid (using esearch). I always get the first
> 10,000 records. For example, I need10,300 gi_ids, I split them into list of
> 10,000 and submit them consecutively and still getting the first 10,000
> records. I tried batch approach in Biopython tutorial, didn't even reach
> 10,000 sequences.
>
> Is there a limit for NCBI's returned sequences?
>
> Thank you.
>
> Mariam

It does sound like you've found some sort of Entrez limit,
it might be worth emailing the NCBI to clarify this.

Have you considered downloading the GI/taxid mapping
table from their FTP site instead? e.g.
http://lists.open-bio.org/pipermail/biopython/2009-June/005295.html

Peter