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

[Scott Markel]

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.

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.

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.

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.

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.

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
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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


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Tuesday, 13 January 2009 9:28 AM
> To: BioPerl List
> Subject: [Bioperl-l] About to tag the last RC...
> 
> All,
> 
> I'm going to run one more RC round for bioperl before the final 1.6
> release; there are some odd test failures on CPAN Testers I'm trying
> to rectify.  I will probably tag/bag/release RC3 sometime this
> afternoon.
> 
> Any complaints?  Issues?  Bugs?  Haven't heard any feedback except
> from Sendu (which is a worry for a stable release).
> 
> chris
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