[Bioperl-l] 1.0alpha this weekend?

Jason Stajich jason@cgt.mc.duke.edu
Tue, 12 Feb 2002 19:21:03 -0500 (EST)

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.

> (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???

* (992) Sub dividing a seqeunce (trunc) and remapping the
        coordinates -- what happens to fuzzies....  we should probably
        support this by making new fuzzies - this was consensus at
* (1038) - the Bio::SeqFeature::Gene objects may have a bug?

* (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.


* (1039) - Misc. Bio::Tools::SeqPattern bug - is it really a bug?
* (1014) - anyone use the Restriction Enzyme pkg and want to check this

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