[Bioperl-l] GenBank format and feature names > 15 char

Chris Fields cjfields at uiuc.edu
Mon Jan 14 14:35:46 EST 2008


It looks like the keys in the feature table run into the location  
string w/o intervening space, which would probably cause havoc with  
roundtripping from this output.  A few examples:

      BAC_cloned_genomic_insert<1..>1000
      combined_genscanjoin(<1..347,400..498,794..>1000)
      splign_na_dbEST_ncbi<1..>1000

I would think at least a space in between the location and the key  
would be required for round-tripping out of genbank format.

chris

On Jan 14, 2008, at 12:53 PM, Lincoln Stein wrote:

> Hi Scott,
>
> He is correct about the limitation, but we deliberately relaxed it  
> because
> we were running into situations where we lost information during
> roundtripping from other formats into genbank.
>
> Lincoln
>
> On Jan 14, 2008 1:46 PM, Scott Cain <cain.cshl at gmail.com> wrote:
>
>> Hi all,
>>
>> Last month, I got a bug report on the GBrowse bug tracker:
>>
>>
>> http://sourceforge.net/tracker/index.php?func=detail&aid=1845217&group_id=27707&atid=391291
>>
>> about a problem with dumping invalid GenBank files.  GBrowse uses
>> Bio::SeqIO::genbank to create these dumps.
>>
>> In his bug report, he claims that feature names over 15 characters  
>> long
>> are invalid, and provided and example GenBank file where a feature is
>> named 'BAC_cloned_genomic_insert', which is over 15 characters.   
>> What I
>> want to know is this: is this truly a restriction on the GenBank  
>> format,
>> or is it a software problem with some other package?  Do we need to  
>> fix
>> genbank.pm?  I'm perfectly willing to do it; I'm just hesitant to
>> believe this is really a bug.
>>
>> Thanks,
>> Scott
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   cain.cshl at gmail.com
>> GMOD Coordinator (http://www.gmod.org/)                      
>> 216-392-3087
>> Cold Spring Harbor Laboratory
>>
>>
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>
>
>
> -- 
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
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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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