[Biopython-dev] [Bug 2468] Tutorial needs a fix: Bio.WWW.NCBI

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2468





------- Comment #3 from mmokrejs at ribosome.natur.cuni.cz  2008-03-17 07:47 EST -------
Hi Peter,
  yes this would be more helpful. Unfortunately I did the one-time job with
parsing the HTML output and re-running wget to fetch the final HTML page,
stripped HTML formatting and was done. I will upload my two crappy scripts.
They work but should be re-written to utilize the XML outputs you have
mentioned.


The second URL from your last comment should have different values for some
parameters to yield another XML page:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=41073&report=sgml&mode=xml

That returns me:

<?xml version="1.0"?>
<!DOCTYPE TaxaSet PUBLIC "-//NLM//DTD Taxon, 14th January 2002//EN"
"http://www.ncbi.nlm.nih.gov/entrez/query/DTD/taxon.dtd">
<TaxaSet>
<Taxon>
  <TaxId>41073</TaxId>
  <Lineage>cellular organisms; Eukaryota; Fungi/Metazoa group; Metazoa;
Eumetazoa; Bilateria; Coelomata; Protostomia; Panarthropoda; Arthropoda;
Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera;
Endopterygota; Coleoptera; Adephaga</Lineage>
  <!-- large cut -->
</Taxon>
</TaxaSet>


Maybe I will find the time to rewrite them for the purpose of tutorial to use
the XMLs.


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