[BioPython] Bio.Entrez and retmax

[Peter Cock]

Hi Pavel,

I've change the subject/title as this isn't about BLAST anymore.

On Wed, Aug 27, 2008 at 10:47 PM, Pavel SRB <srbanator at heckler-koch.cz> wrote:
> hi alex, when i am accessing data like
>
> handle = Entrez.esearch(db="nucleotide", rettype="fasta", retmax=100,
> email=my_email)
>
> i get 100 results, but without i get only 20.

If you look in /usr/share/python-support/python-biopython/Bio/Entrez/__init__.py
or online at http://biopython.org/SRC/biopython/Bio/Entrez/__init__.py
you'll see the
function esearch doesn't set a default value.

I guess that means the NCBI defaults to giving you only 20 unless you
ask for more.

> When looking into
> /usr/share/python-support/python-biopython/Bio/EUtils/ThinClient.py
> there is defaul value for retmax set to 20.

Bio.EUtils is separate from Bio.Entrez, but they both give access to
the NCBI Entrez Utilities.  You should ignore Bio.EUtils as it will be
deprecated in the next release of Biopython.

Peter