[Bioperl-l] 1.0alpha this weekend?

[Ewan Birney]

On Fri, 15 Feb 2002, Steve Chervitz wrote:

> 
> 
> 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 am happy to force/wait for  SearchIO::Writer to remove Blast. The Blast
tools are our biggest maintenance headache ...



> 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 ;).
> 

I'll poke around -- commit if you have anything done and I'll pick it
up. Jason and I will certainy get it done in Cape Town (right Jason?)



> 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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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> 
> 
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-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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