[BioPython] Problem with Entrez?
Sebastian Bassi
sbassi at gmail.com
Sun Aug 24 22:18:09 UTC 2008
>>> handle = Entrez.efetch(db="nucleotide", id="326625")
>>> record = Entrez.read(handle)
Traceback (most recent call last):
File "<pyshell#13>", line 1, in <module>
record = Entrez.read(handle)
File "/mnt/hda2/py252/lib/python2.5/site-packages/Bio/Entrez/__init__.py",
line 283, in read
record = handler.run(handle)
File "/mnt/hda2/py252/lib/python2.5/site-packages/Bio/Entrez/Parser.py",
line 95, in run
self.parser.ParseFile(handle)
ExpatError: syntax error: line 1, column 0
So I efetch it again just to show the format of handle:
>>> handle = Entrez.efetch(db="nucleotide", id="326625")
>>> print handle.read()[:200]
Seq-entry ::= seq {
id {
genbank {
name "HIVED82FO" ,
accession "M77599" ,
version 1 } ,
gi 326625 } ,
descr {
title "Human immunodeficiency virus type 1 gp120 (env)
Looks like ASN1 format, but according to the tutorial efetch should
return its output in XML format:
"By default you get the output in XML format, which you can parse
using the Bio.Entrez.read() function "
As a workaround I specify the format with rettype='gb'
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