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

Lincoln Stein lstein at cshl.edu
Mon Jan 14 14:46:20 EST 2008


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
> >>
> >>
> >> _______________________________________________
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> >> 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
>
>
>
>


-- 
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


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