[Bioperl-l] About to tag the last RC...

[Scott Markel]

Chris,

Thank you for the quick reply, the changes, and for all of your work
to get 1.6 ready.

Scott


> -----Original Message-----
> From: Chris Fields [mailto:cjfields at illinois.edu]
> Sent: Wednesday, 14 January 2009 9:18 PM
> To: Scott Markel
> Cc: BioPerl List; Kristine Briedis
> Subject: Re: [Bioperl-l] About to tag the last RC...
> 
> On Jan 14, 2009, at 5:45 PM, Scott Markel wrote:
> 
> > Chris,
> >
> > We've been testing 1.6 RC2 with our set of nightly Pipeline Pilot
> > regressions and have noticed a few issues.  Sorry we couldn't get
> > this feedback to you sooner.
> >
> > 1) There is a problem with the output filename for bl2seq on
> > Windows.  In response to bug 2707, quotemeta was used when building
> > the parameter string at line 507 in
> > Bio::Tools::Run::StandAloneNCBIBlast (1.5.9_2).  This causes a
> > problem with the path to the output file on Windows.  For example,
> > "C:\DOCUME~1\outfile" becomes "C\:\\DOCUME\~1\\outfile".  bl2seq
> > can't open the output file and fails.
> 
> I've added an OS check for that so this isn't used with Windows (I
> wondered whether quotemeta would bite me there).  I'm seriously
> considering ripping out that code altogether, though.  I'm not sure we
> want to wade into attempting to accurately escape shell chars simply
> based on OS differences.
> 
> > 2) Parsing megablast output (format 2) with Bio::SearchIO::blast.pm
> > now returns an algorithm name of "BLASTN" instead of "MEGABLAST".
> > This change seems to have been introduced in revision 11579 of
> > blast.pm when a couple regex changes were made (lines 452 and 1201
> > of blast.pm in 1.5.9_2).  Subbing in the old regular expression for
> > megablast in line 452 returned the correct "MEGABLAST" algorithm name.
> 
> I worked out why that regex isn't working (it doesn't match MEGABLAST
> at all).  I fixed it and added a test for checking the algorithm to
> the test suite for MEGABLAST output, seems to work now.
> 
> > We also see some minor differences that we can live with, e.g.,
> > BLAST hit scores changing from 40 to 40.1 and e-values having
> > trailing zeros.  We'll just update our baselines.
> 
> Okay, but let me know if that becomes pressing.  The e-value issue is
> a bit odd and may be worth looking into.
> 
> > The change to using Bio::Annotation::TagTree for SwissProt sequence
> > gene names broke a number of our tests but we'll fix that by
> > modifying the adapters we use between our internal representation
> > and BioPerl's.
> 
> That would be from the switchover from StructureValue (which wasn't
> really designed for the purposes of storing such data).  A layered
> Bio::Annotation::Collection was the other option (this is almost a
> light version of that).
> 
> > One thing we haven't tracked down yet is a change in tag type, e.g.,
> > b:integervalue to b:stringvalue, in the XML representations of our
> > Pipeline Pilot data records.  We're only seeing this for programs in
> > NCBI's BLAST suite.  At this point we don't know what's changed on
> > the BioPerl side to trigger the change in our code.  We'll continue
> > to investigate this.
> 
> Again, if you find it's on our side let us know.
> 
> > Scott
> >
> > Scott Markel, Ph.D.
> > Principal Bioinformatics Architect  email:  smarkel at accelrys.com
> > Accelrys (SciTegic R&D)             mobile: +1 858 205 3653
> > 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
> > San Diego, CA 92121                 fax:    +1 858 799 5222
> > USA                                 web:    http://www.accelrys.com
> >
> > http://www.linkedin.com/in/smarkel
> > Board of Directors: International Society for Computational Biology
> > Co-chair: ISCB Publications Committee
> > Associate Editor: PLoS Computational Biology
> > Editorial Board: Briefings in Bioinformatics
> 
> Thanks Scott!  Let us know if you have any other problems.  I've been
> busier than expected but should get RC3 out soon.
> 
> -c