[Bioperl-l] bp_search2gff.pl

[Eric Just]

Thanks Chris, I'll enter it as a bug.  I'd also be glad to help on the
solution if there is an executive decision made at some point.



On 10/5/07, Chris Fields <cjfields at uiuc.edu> wrote:
> We might want to file this as a bug so we can track it.
>
> The core devs have been mulling over the state of GFF/GFF3 in
> BioPerl; proper handling of any SearchIO data is certainly included
> in that.  I believe some road forward is to be planned soon (after
> Genome Informatics).
>
> chris
>
> On Oct 5, 2007, at 2:35 PM, Eric Just wrote:
>
> > Hello,
> >
> > I have been playing with the bp_search2gff.pl script (on HEAD of
> > bioperl-live).    There are a couple of issues I was wondering about.
> >
> > One is the ID that gets generated for a match feature when the --match
> > option is set.   The ID is  set to the ID of the query sequence.  This
> > can be problematic if you are representing the query sequence and the
> > blast hit in the same gff file.  When using the resultant gff file for
> > loading into Chado, it also creates a problem if you have more than
> > one hit for a given query sequence, for example if you ran two
> > different analyses that each had a hit for a given query.  Would it be
> > possible to have an option to create a unique ID for match features.
> > One suggestion could be to create an ID based on the ID of the query +
> > the id of the hit + the source
> >
> > As long as two different analyses were loaded as different sources,
> > this would ensure unique IDs for the match features.
> >
> >
> > Also, is there a reason for writing the Target string as
> >
> > Target=Sequence:SOME_ID
> >
> > as opposed to
> >
> > Target=SOME_ID
> >
> >
> > The latter seems a little more in line with the gff3 spec and plays a
> > little nicer with the GMOD tools.
> >
> > Thanks for looking into this.
> >
> > Eric
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>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>