[Biopython] can I use the xml parser in biopython on other xml files? how?
Wheaton Little
wheatontrue at gmail.com
Thu Jul 12 08:53:26 UTC 2012
I would like to use the Biopython xml parser, if possible, on google
patent xmls:
http://www.google.com/googlebooks/uspto-patents-applications-text.html
unfortunately, this is what I get:
>>> t=open('ipa111229.xml','r').read()
>>> import Bio
>>> ttt=Bio.Entrez.read(t[:30000])
Traceback (most recent call last):
File "<pyshell#20>", line 1, in <module>
ttt=Bio.Entrez.read(t[:30000])
File "/Library/Python/2.7/site-packages/Bio/Entrez/__init__.py",
line 351, in read
record = handler.read(handle)
File "/Library/Python/2.7/site-packages/Bio/Entrez/Parser.py", line
169, in read
self.parser.ParseFile(handle)
TypeError: argument must have 'read' attribute
What would I have to do to use the parser on this xml?
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