[Bioperl-l] Developers: what do you want to fix before 1.4 release?

[Jason Stajich]

> P.S.1. Other open bugs related to SearchIO are: 1416, 1418, 1468, 1558

Happy pre-Thanksgiving ....

1558 - Fixed.
1416 - Fixed. good enough, I can't reproduce it
1418 - Fixed. I think it works, I have started just using Guy's GFF output
       but I think it all matches up with parse from his VULGAR
       strings

Not quite there:
1468 - It seems to work okay now.  Everything except printing the
       Statistics in the BLAST way.
       Something that can be done without too much work I think.

>
> P.S.2. Also thanks for spotting the wrong URL.
>
>
> On Tuesday 25 Nov 2003 TT:10, Steve Chervitz wrote:
> > On Nov 24, 2003, at 2:04 PM, Jason Stajich wrote:
> > > I am fixing up blast parsing to get the gapped, ungapped, and
> > > frame-specific lambda,kappa, entropy from the reports for those who
> > > want
> > > this.  I will also try and make sure we are getting more of the
> > > parameters
> > > from the reports into the Result objects.
> > >
> > > Presumably we had talked about remove SearchIO/psiblast.pm from 1.4
> > > release - not sure if that is still a good idea.
> >
> > I'm fine with this. There are a few example scripts that are pointing
> > at psiblast.pm. We'll have to make sure they work with blast.pm.
> >
> > SearchIO/psiblast.pm depends on some modules in Bio::Tools that can
> > probably also go away (Bio::Tools::StateMachine::*) since these modules
> > aren't being used by any other Bioperl modules. There may be external
> > code that depends on them, but not too likely. If there's interest, I
> > could contribute them separately to CPAN.
> >
> > Steve
> >
> > > I also have some more work on the PopGen objects to make sure all the
> > > numbers are correct for some of the implemented tests.
> > >
> > > -jason
> > >
> > > On Mon, 24 Nov 2003, Heikki Lehvaslaiho wrote:
> > >> With developer snapshot 1.3.03 out last Friday, I'd like to hear from
> > >> bioperl
> > >> developers what they'd like to accomplish before 1.4 comes out.
> > >>
> > >> At this stage, I'd rather not see major new features added; there
> > >> will not be
> > >> time to test them properly.
> > >>
> > >> I'd especially like to hear from
> > >> * Lincoln Stein / Todd Harris about the SVG timetable
> > >> * Stefan Kirov about Bio::Matrix::PSM modules
> > >> * anyone else about their pet modules and bugs
> > >>
> > >> I'll give you three choices:
> > >>
> > >> 1. You've got a fix/enhancement under way and you can give me
> > >> timetable
> > >> for it to be in.
> > >>
> > >> 2. There is a bug that need to be fixed before the release but you do
> > >> not know how to do it.  Let's discuss that now!
> > >>
> > >> 3. Your modules are not ready for release and you do not have time to
> > >> work on your code. That means that they will need to be excluded from
> > >> the release.
> > >>
> > >> I am pretty happy with the current status of bioperl CVS tree. Tests
> > >> pass, but there still are bugs in bugzilla. I urge anyone and everyone
> > >> to have a look at the bugzilla and see what they think of the bugs
> > >> still
> > >> there.
> > >>
> > >> Realistically, we have couple of weeks time to get the fixes in. Then
> > >> a
> > >> week to wait to make sure everyone has time to make sure that
> > >> everything
> > >> works.
> > >>
> > >> 	-Heikki "Let's push 1.4 out"
> > >
> > > --
> > > Jason Stajich
> > > Duke University
> > > jason at cgt.mc.duke.edu
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>

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