[Biopython] [Entrez] use the handle twice

c.buhtz at posteo.jp c.buhtz at posteo.jp
Sat Dec 19 12:41:59 UTC 2015


On 2015-12-19 11:06 Peter Cock <p.j.a.cock at googlemail.com> wrote:
> This is the way network handles work, the server returns
> the data to the client computer (your Python code) once
> only. As soon as you read it (or Biopython's parser does),
> the data is gone.

Then make it possible to cache the informations.
UndoHandle? Find the API-reference but not a docu with examples how to
use this.

> For large data, the best plan is simply to save the data
> to a file on disk, then reopen the file for reading and
> parse it.

I see no way to do this. e.g.

import Bio.Entrez
import zipfile

z = zipfile.ZipFile('test.zip')
h = z.read( z.namelist()[0] )
r = Bio.Entrez.parse(h)

Now r is a generator and I can not ask things like that
 r['Count']

And Bio.Entrez.read(h) doesn't work here - don't understand why.

I just want to know how much records really are comin back from the
server.
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