[BioPython] SwissProt parse error

[Michael Sierk]

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;


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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
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"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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