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

Scott Cain cain.cshl at gmail.com
Tue Jan 15 21:24:50 EST 2008


Hi Chris and Lincoln,

I've attached my suggested patch.  So, can I use svn to check it in?  It
only adds a space after the feature type name; I suspect that will be
enough to fix the file format for most uses.

Scott

On Mon, 2008-01-14 at 14:46 -0500, Lincoln Stein wrote:
> That's a new bug. The version I worked on inserted a space after the name.
> 
> Lincoln
> 
> On Jan 14, 2008 2:35 PM, Chris Fields <cjfields at uiuc.edu> wrote:
> 
> > 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
> > >>
> > >>
> > >> _______________________________________________
> > >> Bioperl-l mailing list
> > >> Bioperl-l at lists.open-bio.org
> > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > >>
> > >
> > >
> > >
> > > --
> > > Lincoln D. Stein
> > > Cold Spring Harbor Laboratory
> > > 1 Bungtown Road
> > > Cold Spring Harbor, NY 11724
> > > (516) 367-8380 (voice)
> > > (516) 367-8389 (fax)
> > > FOR URGENT MESSAGES & SCHEDULING,
> > > PLEASE CONTACT MY ASSISTANT,
> > > SANDRA MICHELSEN, AT michelse at cshl.edu
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> >
> 
> 
-- 
------------------------------------------------------------------------
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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