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<div class="">The way I have traditionally done this (in bioperl) is to iterate through 500 at a time, setting retmax to 500 and varying the offset using retstart, appending records to the same file when they aren’t raw XML (e.g. seq records). Otherwise I
loop through and use the objects created from the XML->object mapping to grab the information I care about. I expect the same is possible via Biopython.</div>
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<div class="">chris</div>
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<div class="">On Dec 2, 2015, at 4:04 PM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" class="">p.j.a.cock@googlemail.com</a>> wrote:</div>
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<div dir="ltr" class="">Hi,
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<div class="">Currently Biopython does not attempt to do anything about</div>
<div class="">limiting retmax on your behalf. The suggested retmax limit of 500</div>
<div class="">is probably specific to that database and/or file format (or so I</div>
<div class="">would imagine - some records like uilists are tiny in comparison).</div>
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<div class="">Are you using the results as XML? It probably is possible to</div>
<div class="">merge the XML files, but it might be more hassle that its worth.</div>
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<div class="">I would suggest a double loop ought to work fine - loop over</div>
<div class="">the collection of XML files, and then for each file loop over the</div>
<div class="">records returned from the parser.</div>
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<div class="">Regards,</div>
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<div class="">Peter<br class="">
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Wed, Dec 2, 2015 at 9:39 PM, <span dir="ltr" class="">
<<a href="mailto:c.buhtz@posteo.jp" target="_blank" class="">c.buhtz@posteo.jp</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I asked the Entrez support how should I tread the servers resources<br class="">
with "respect". :)<br class="">
<br class="">
First answer was without discrete numbers but in the second one they<br class="">
told me asking for 500 (retmax for eSearch) is a "reasonable" value<br class="">
because the eBot (a tool they offer on their website) use it, too.<br class="">
<br class="">
No I have nearly 13.000 PIDs I want to fetch their article infos via<br class="">
eFetch. It is a lot. ;)<br class="">
<br class="">
But I am not sure how to do that with biopython. When I separate that<br class="">
in 500-packages I would have 26 different record objects back.<br class="">
I don't like that. I would prefer one big record object I can analyse.<br class="">
<br class="">
Do you see a way to merge this record objects. Or maybe there is<br class="">
another way for that?<br class="">
Or does Biopython.Entrez still handle that problem internal (like the<br class="">
only-3-per-second-querys-rule or the HTTP-POST-decision)?<br class="">
<br class="">
Any suggestions?<br class="">
<span class="HOEnZb"><font color="#888888" class="">--<br class="">
GnuPGP-Key ID 0751A8EC<br class="">
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