[Biopython] Problem using efetch

Tue Jul 14 15:39:08 UTC 2009

Hi,

I’m using BioPython to access Entrez databases.  I’m following the BioPython
tutorial.
I’ve tried retrieving all record ids from pcassay database with esearch and
then retrieving the first full record on the list with efetch:

handle = Entrez.esearch(db="pcassay", term="ALL[filt]")

print record["IdList"]

# This prints the following list of ids:

# ['1866', '1865', '1864', '1863', '1862', '1861', '1033', '1860', etc.

But when I then try to retrieve the first record:

handle2 = Entrez.efetch(db="pcassay", id="1866")

I get the following error :

<html>

<body>

<br/><h2>Error occurred: Report 'ASN1' not found in 'pcassay'
presentation</h2><br/><ul title="some params from request:">

<li>db=pcassay</li>

<li>query_key=</li>

<li>report=</li>

<li>dispstart=</li>

<li>dispmax=</li>

<li>mode=html</li>

<li>WebEnv=</li>

</ul>

<br/><b>pmfetch need params:</b><br/><br/>

<li>(id=NNNNNN[,NNNN,etc]) or (query_key=NNN, where NNN - number in the
history, 0 - clipboard content for current database)</li>

<li>db=db_name (mandatory)</li>

<li>report=[docsum, brief, abstract, citation, medline, asn.1, mlasn1,
uilist, sgml, gen] (Optional; default is asn.1)</li>

<li>mode=[html, file, text, asn.1, xml] (Optional; default is html)</li>

<li>dispstart - first element to display, from 0 to count - 1, (Optional;
default is 0)</li>

<li>dispmax - number of items to display (Optional; default is all elements,
from dispstart)</li>

<br/>See <a href="
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html
">help</a>.</body>

</html>

Do you have an idea of what I’m doing wrong?

Thanks very much