[Biopython] Issue with Bio.Entrez and protein in Biopython 1.60
Cristian Alejandro Rojas
alejandro.0317 at gmail.com
Fri Jan 25 20:16:42 EST 2013
Hi all.
I'm having a issue using Bio.Entrez to search a protein. I'm doing this:
>>> handle=Entrez.esearch(db="protein", term="insulin AND homo")
>>> record=Entrez.read(handle)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/pymodules/python2.7/Bio/Entrez/__init__.py", line 351, in
read
record = handler.read(handle)
File "/usr/lib/pymodules/python2.7/Bio/Entrez/Parser.py", line 169, in
read
self.parser.ParseFile(handle)
File "/usr/lib/pymodules/python2.7/Bio/Entrez/Parser.py", line 307, in
endElementHandler
raise RuntimeError(value)
RuntimeError: Search Backend failed: Database is not supported: protein
I'm having a issue with einfo() too, check at this:
>>> handler=Entrez.einfo(db="protein")
>>> record=Entrez.read(handler)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/pymodules/python2.7/Bio/Entrez/__init__.py", line 351, in
read
record = handler.read(handle)
File "/usr/lib/pymodules/python2.7/Bio/Entrez/Parser.py", line 169, in
read
self.parser.ParseFile(handle)
File "/usr/lib/pymodules/python2.7/Bio/Entrez/Parser.py", line 285, in
startElementHandler
raise ValidationError(name)
Bio.Entrez.Parser.ValidationError: Failed to find tag 'Build' in the DTD.
To skip all tags that are not represented in the DTD, please call
Bio.Entrez.read or Bio.Entrez.parse with validate=False.
Why protein database is not supported?, Can somebody help me with this
issue?
Grettings!
--
*Cristian Alejandro Rojas Quintero*
*Estudiante Ingeniería de Sistemas *
*Universidad Distrital Francisco José de Caldas*
Bogotá - Colombia
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