[Bioperl-l] Re: problems with Bio::Tools::GFF

[Jason Stajich]

Feel free to fix it to spec Scott.

Note that I have also made no attempt to parse/write the Gap or Alignment
stuff in any sort of special way - I basically made it so it supports what
GFF2 currently looks like only in GFF3 flavor.  Perhaps it makes sense to
do all of that work on Chris's Unflattner though rather than in
Tools::GFF.  A SeqFeature::Tools::Flattner is probably in order as well to
turn HSPs and other paired sequences into GFF3 Alignments.

As for the seq stuff - will likely need a Bio::SeqIO::gff3 for that.

Anyone is welcome to add these changes - I don't think I'll be able to
make many contributions until December so it would be best if someone else
took it on.

-jason

On Mon, 3 Nov 2003, Scott Cain wrote:

> Hi Jason and Lincoln,
>
> I have a few concerns with Bio::Tools::GFF. The first is with the method
> _from_gff3_string, which does a split on \t to separate columns.  I
> think the GFF3 spec says it can be space delimited, so that should
> probably be \s+.  Additionally, to split the groups column, it uses
> \s*;\s*, but I think that spaces have to be escaped, therefore, it
> should only split on ; and spaces would indicate a problem (especially
> if one splits on spaces as indicated above).
>
> Finally, it doesn't provide a method of accessing the sequence that is
> optionally at the bottom of the file.  I am not exactly sure how to
> implement that (or I would), but I suspect it will have to be handled in
> the next_feature method.  Of course, the problem with handling it there
> is that it is not a feature.
>
> Scott
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu