[Bioperl-l] 1.0alpha this weekend?

[Steve Chervitz]

Jason Stajich <jason@cgt.mc.duke.edu> wrote:

> On Tue, 12 Feb 2002, Ewan Birney wrote:
> 
> >
> >
> > With Peter's and Brian's documentation fixes in I would like to propose a
> > 1.0alpha release this coming weekend.
> >
> >
> > (a) Could code reviewers (myself included) review code
> >
> >
> > (b) Jason/Mark --- are the issues with SearchIO resolved?
> >
> yep - he just wanted to be able to reset the iterator - (after i fixed the
> silly blastn parsing bug).
> 
> >
> > (c) I would like to propose removing Bio::Tools::BLAST and replacing it
> > with a module which simply throws an exception on new describing how to
> > use the SearchIO system
> >
> yeah - and can we agree the BPlite is in the twilight - we'll plan to
> provide bug fixes on BPlite but development effort will be focused on
> SearchIO unless someone REALLY wants to be its maintainer.

I'd prefer if we keep Bio::Tools::Blast and make a deprecation warning appear when
anyone calls its new() method. The message can also point people at SearchIO. 

The reason not to remove it entirely is that there is still some functionality that
has not been migrated to SearchIO, primarily the to_html() method. The plan is to
replace this with the SearchIO::Writer system.

I can make an attempt to get the to_html() stuff migrated over this weekend, but as
I'm currently attending the MGED4 meeting in Boston, I can't guarantee. (If I have
sufficient battery power, I may be able to get it done on the plane ;).

There may be other useful tidbits in Bio::Tools::Blast still lingering. I'll need
some time to check against what's in SearchIO.


> >
> > (d) Lincoln - you said you wanted to run all of genbank through the SeqIO
> > system?
> >
> >
> >
> >
> > any other thoughts out there?
> >
> 
> There are 26 bugs in the queue some of them are not going to get done in
> this releae I suspect, but many of them are straightforward. Would be nice
> to take a look and see what can get fixed.
> 
> 
> The highlights of what is in the queue, volunteers needed to test and fix
> these bugs.  Your contribution could just be to provide a reproduceable
> script (and datafile where needed) for the bug.
> 
> 
> Cross-Platform / Execing programs
> * (966) Tools::Run::Alignment modules
> * Platform dependent issues (906) Mac and (1052) Windows+Clustalw.  Not
>   sure I want to fix 1052 as suggested.
> * (986) Tempfiles and cleanup - do we want to do a migratio to IO::File
>         from File::Temp???
> 
> SeqFeatures
> * (992) Sub dividing a seqeunce (trunc) and remapping the
>         seqfeature
>         coordinates -- what happens to fuzzies....  we should probably
>         support this by making new fuzzies - this was consensus at
>         hackathon.
> * (1038) - the Bio::SeqFeature::Gene objects may have a bug?
> 
> SeqIO
> * (876) decide if we want to do any PIR support - the module had been
>   updated, not sure it is completely compliant.
> * (987) SCF bug which should be gone with Chad's new implementation
> * (1000) - EMBL bug that is fixed on main-branch - can we remove (are we
>            ever going to do another 0.7 series release?)
> * (1043,1062,1068,1069) genbank parsing, (1071) swissprot writing
>   [ I tested 1043 and it is definitely there]
>   Are we really writing in the new GenBank format - can we really parse
>   the new genbank format properly?
>   I also may have lost Emmanuel's bug wrt to SwissProt unless Allen fixed
>   it in his SwissProt.
> 
> Misc
> 
> * (1039) - Misc. Bio::Tools::SeqPattern bug - is it really a bug?
> * (1014) - anyone use the Restriction Enzyme pkg and want to check this
>            out?

As these were my babies, I can have a look see. I recently made some fixes and
modifications to RestrictionEnzyme, so I may have this bug covered.

Steve
--
Steve Chervitz
sac@bioperl.org

> Analysis Result parsing /SearchIO
> * (1034) - possible HMMer parsing bug (are we going to move HMMer parsing
>            into SearchIO for 1.0?)
> * (1025) - BPlite parsing issues, BPlite out of memory issues (1039) -
>            probably due to tempfile issues with File::Temp
> * (1063) - SearchIO blast parsing an empty report - may be fixed already
>            - just need a tester?
> 
> 
> >
> >
> >
> >
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>.
> > -----------------------------------------------------------------
> >
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> >
> 
> -- 
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
> 
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