[BioPython] SwissProt parse error

[Michael Sierk]

The parsing problem is solved.  Thanks!

Mike

On Sep 8, 2004, at 5:49 PM, Jeffrey Chang wrote:

> Hi Mike,
>
> Yes, what Iddo said.  Please grab the latest SProt.py code from the  
> latest CVS (cvs.biopython.org) and see if that solves your problem.   
> Also, I have committed a fix today to handle recent format changes in  
> swiss-prot, that was reported in personal correspondence by Daan  
> Archer.  They have added an "RG" field.  I don't know whether that is  
> causing the problem.  If not, please let us know what swiss-prot  
> record is failing to parse.
>
> Thanks,
> Jeff
>
>
> On Sep 8, 2004, at 1:50 PM, Iddo wrote:
>
>>
>> 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.
>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
>>> +++ +++++++
>>>
>>> _______________________________________________
>>> BioPython mailing list  -  BioPython at biopython.org
>>> http://biopython.org/mailman/listinfo/biopython
>>>
>>>
>>
>>
>> -- 
>> 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
>>
>> _______________________________________________
>> BioPython mailing list  -  BioPython at biopython.org
>> http://biopython.org/mailman/listinfo/biopython
>>
>
>

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
+++++++
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.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
+++++++