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

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





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2008-03-13 07:27 EST -------
Reading the Bio.Entrez documentation, the query function always returns HTML. 
You could also use the esearch function which returns XML, followed by the
efetch function which seems to support a range of options depending on the
datatype.  For example, using the taxonomy db:

#This gets an XML file from the following URL,
#http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=Cypripedioideae
from Bio import Entrez
result_handle = Entrez.esearch("taxonomy", term="Cypripedioideae")
print result_handle.read()

You could then parse the XML file to extract the matching ID(s), perhaps with a
regular expression.  In this case, there is only one match, 158330.

#http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy
#&id=9685&report=brief&retmode=text
from Bio import Entrez
result_handle = Entrez.efetch("taxonomy", id="158330", \
                              report="docsum", retmode="text")
print result_handle.read()
#Given ID 9685, returns "Cypripedioideae, subfamily, monocots"

I agree that this section of the tutorial could be more useful.  Do you think
the above could would be more helpful?


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