[Bioperl-l] About to tag the last RC...
SMarkel at accelrys.com
Thu Jan 15 09:14:50 EST 2009
Thank you for the quick reply, the changes, and for all of your work
to get 1.6 ready.
> -----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.
More information about the Bioperl-l