[Bioperl-l] possible bug printing GenBank feature qualfiers

Chris Fields cjfields at uiuc.edu
Fri Mar 31 22:16:22 EST 2006


On Mar 31, 2006, at 5:02 PM, Hilmar Lapp wrote:

> Note that GenBank requires a 'source' feature. The GenBank parser uses
> it to get the NBCI taxon ID (as that is the feature where it will be
> given as a db_xref tag). I thought the parser wouldn't mandate the
> feature but maybe at some point it assumes that it's there. Need to
> check, just a speculation.

Right, but if this were the case shouldn't converting from a simple  
format (one lacking most annotation and feature information,  
including a source, like fasta) to genbank raise all sorts of  
warnings?  I get this conversion to work without errors or warnings,  
though there doesn't seem to be any attempt by SeqIO to check the  
fasta header line for accessions, etc. (a separate issue which I  
think Jason mentioned a fix for; I guess it hasn't been implemented  
yet).  No source line is in the output sequence either.

Chris

> On 3/31/06, Brian Osborne <osborne1 at optonline.net> wrote:
>> Chris,
>>
>> Not OS-specific, I also see "no feature key!" on Mac OS.
>>
>> Brian O.
>>
>>
>> On 3/31/06 3:27 PM, "Chris Fields" <cjfields at uiuc.edu> wrote:
>>
>>> I wouldn't be a bit surprised if it is a WinXP-specific issue, so  
>>> I'll give
>>> it a try this weekend on Mac OS X using the latest CVS to see  
>>> what happens.
>>
>>
>>
>
>
> --
> ----------------------------------------------------------
> : Hilmar Lapp -:- San Diego, CA -:- hlapp at gmx dot net :
> ----------------------------------------------------------

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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