[BioPython] about GenBank module...

[Jeffrey Chang]

Hi ky,

Which version of Biopython are you using?  I am having trouble  
duplicating your report.

 >>> from Bio import GenBank
 >>> gi_list = GenBank.search_for("opuntia AND rpl16")
 >>> len(gi_list)
7
 >>> print gi_list
['6273291', '6273290', '6273289', '6273287', '6273286', '6273285',  
'6273284']
 >>>

Jeff


On Jan 24, 2004, at 10:10 AM, Ka-Young An wrote:

> Hi,
>
> I have very simple problem,,,
>
> When I use the GenBank module,,the following code doesn't work...
> (the otherthing like swissport or pubmed is working well..)
>
> I think this sourse don't have any syntax problem,,
>
> so..pleas let me know..what is the problem...
>
> ____________________________________________________________
> (line1) from Bio import GenBank
> (line2)
> (line3) gi_list = GenBank.search_for("Opuntia AND rpl16")
> _____________________________________________________________
>
>
> There are some error message like this....
>
> ____________________________________________________________________
> Traceback (most recent call last):
>   File "C:\Documents and Settings\kayounga\Desktop\lovepython\a.py",  
> line
> 3, in ?
>     gi_list = GenBank.search_for("Opuntia AND rpl16")
>   File "C:\Python22\lib\site-packages\Bio\GenBank\__init__.py", line  
> 1609,
> in search_for
>     parser.feed(handle.read())
>   File "C:\Python22\lib\sgmllib.py", line 95, in feed
>     self.goahead(0)
>   File "C:\Python22\lib\sgmllib.py", line 129, in goahead
>     k = self.parse_starttag(i)
>   File "C:\Python22\lib\sgmllib.py", line 290, in parse_starttag
>     self.finish_starttag(tag, attrs)
>   File "C:\Python22\lib\sgmllib.py", line 328, in finish_starttag
>     self.handle_starttag(tag, method, attrs)
>   File "C:\Python22\lib\sgmllib.py", line 364, in handle_starttag
>     method(attrs)
>   File "C:\Python22\lib\site-packages\Bio\GenBank\__init__.py", line  
> 1600,
> in start_a
>     for name, value in params:
> ValueError: unpack list of wrong size
>
> _______________________________________________________________________ 
> ___
>
> Thanks~~
>
> from ky
>
>
> _______________________________________________
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