[BioPython] SwissProt parse error

[Iddo]

Hey Mike,

Asa was using an old version of biopython, and that sorted itself out. 
However,  he was parsing a local file. Are you parsing a local or one 
you are reading from the ExPasy website?

Anyhow, if you email me a bare-bones version of your source code, I'll 
have a looksee.

Iddo


The problem then was that Asa was using an old version... but if you

Michael Sierk wrote:

> Hello, all,
>
> I'm getting the same error reported last year by Asa Ben Hur (  
> http://portal.open-bio.org/pipermail/biopython/2003-June/001411.html ).
> I just installed biopython a few weeks ago, and am a newbie with  
> python/biopython.  Any suggestions?
>
> Thanks,
> Mike Sierk
>
>> wrpmg4b:~ % python disulfides2.py test_seqs.aln
>> Swissprot ID:  Q14063
>> Traceback (most recent call last):
>>   File "disulfides2.py", line 73, in ?
>>     seq_record = get_sprot_entry_remote(seq_id)
>>   File "disulfides2.py", line 26, in get_sprot_entry_remote
>>     entry = iterator.next()
>>   File  
>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 166, in next
>>     return self._parser.parse(File.StringHandle(data))
>>   File  
>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 290, in parse
>>     self._scanner.feed(handle, self._consumer)
>>   File  
>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 333, in feed
>>     self._scan_record(uhandle, consumer)
>>   File  
>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 338, in  
>> _scan_record
>>     fn(self, uhandle, consumer)
>>   File  
>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 414, in  
>> _scan_reference
>>     self._scan_ra(uhandle, consumer)
>>   File  
>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 436, in _scan_ra
>>     one_or_more=1)
>>   File  
>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
>> python2.3/site-packages/Bio/SwissProt/SProt.py", line 360, in  
>> _scan_line
>>     read_and_call(uhandle, event_fn, start=line_type)
>>   File  
>> "/System/Library/Frameworks/Python.framework/Versions/2.3/lib/ 
>> python2.3/site-packages/Bio/ParserSupport.py", line 300, in  
>> read_and_call
>>     raise SyntaxError, errmsg
>> SyntaxError: Line does not start with 'RA':
>> RX   DOI=10.1146/annurev.nutr.22.012502.114457;
>
>
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> +++++++
> Michael Sierk, Postdoctoral Fellow             email:  
> mls5w<AT>virginia<dot>edu
> Biochemistry & Molecular Genetics Dept.    Phone (W): (434) 924-2821
> University of Virginia                           (H): (434) 970-2268
> ------------------------------------------------------------------------ 
> ------
> "There is something fascinating about science. One gets such wholesome
> returns of conjecture out of such a trifling investment of fact."
> -- Mark Twain.
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> +++++++
>
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>
>


-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo