[Bioperl-l] [BioPython] Cannot parse GenBank file

Chris Fields cjfields at uiuc.edu
Tue Jun 5 11:28:24 EDT 2007


Martin,

The example file you give in the bioperl bugzilla report has several  
blank annotation lines which may lead to additional problems.  When  
the BioPerl SeqIO parser finds annotation fields (SOURCE, ORGANISM,  
DEFINITION, etc) then it expects there will also be relevant data  
(text descriptions) accompanying it; I assume the BioPython parser  
expects likewise though I may be wrong.

AFAIK the inclusion of field names w/o text isn't GenBank/EMBL- 
compliant.  GenBank records lacking text either have a '.' instead or  
are left out entirely:

http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html

We could add a fix but you should probably contact the ApE developers  
and request that field names w/o text be left out or have '.' added.

chris

On Jun 5, 2007, at 9:04 AM, Martin MOKREJŠ wrote:

> Ezequiel Panepucci wrote:
>>>     genbank entry = parser.parse(fhandle)
>>
>> there is a space character between "genbank" and "entry".
>> It is a syntax error.
>> I suppose you meant "genbank_entry" ?
>
> Yes, the next command was right and has shown the error. Sorry, I  
> forgot
> to delete the first attempt. ;-)
>
>>>> genbank_entry = parser.parse(fhandle)
> Traceback (most recent call last):
>  File "<stdin>", line 1, in ?
>  File "/usr/lib/python2.4/site-packages/Bio/GenBank/__init__.py",  
> line 187, in parse
>    self._scanner.feed(handle, self._consumer)
>  File "/usr/lib/python2.4/site-packages/Bio/GenBank/Scanner.py",  
> line 360, in feed
>    self._feed_first_line(consumer, self.line)
>  File "/usr/lib/python2.4/site-packages/Bio/GenBank/Scanner.py",  
> line 835, in _feed_first_line
>    assert False, \
> AssertionError: Did not recognise the LOCUS line layout:
> LOCUS               6499 bp ds-DNA     linear       02-AUG-2006
>
>>>>
>
> Martin
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






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