[Bioperl-l] List Summary for Dec 2-8 2002

[Nathan Torkington]

Mailing list summary for bioperl-l
Subscription information: http://www.bioperl.org/MailList.shtml
Period: December 2-8, 2002

** Announcements

Harry Mangalam announced O'Reilly's 2003 Bioinformatics Technology
Conference, February 3-6, 2003 in San Diego, California.
  http://conferences.oreilly.com/bio2003/

** Code Changes

Progress toward 1.2 (deadline Dec 31) came fast and furious.

Bio::Tools::RemoteBlast moved back into core.  There was a long
discussion about creating a bioperl-retired for legacy modules
such as Bio::Tools::Blast.pm (which isn't the module you should
be using to do Blast work).

Jason said that HMMer parsing is "more robustly being tested".

Steve Chervitz was to have added psiblast parsing functionality to
blast.pm so psiblast.pm can be obsoleted for 1.2.  In his words "I'm
having doubts because it is a fairly major undertaking, and there's
time pressure to release 1.2."  Ewan concurred: "I think this has to
happen in the 1.3 to 1.4 series."

Elia will handle bioperl-run regression testing against the 1.2 core
as it solidifies.

Ewan committed reorganized documentation for Bio::Seq, Bio::SeqI,
Bio::PrimarySeqI and Bio::PrimarySeq to stress that Bio::Seq has the
best docs and is the best starting point for users.

Paul Boutros posted a great summary of 'make test' for the current
BioPerl on Windows.

** Unanswered Questions

Allen Day asked whether anyone was working on a script to load GO
terms into chado.

James Wasmuth had a problem with queries and hits that nobody replied
to.

** Bugs

Jason Stajich posted an update to the MakeMaker bug--no immediate
solution, a simple workaround, and a plea for more people to hack on
MakeMaker.

Lincoln went back and forth with Paul Boutros trying to track down a
Bio::DB::Query problem under Windows.  Paul found the problem and
Lincoln supplied a fix that made it pass all tests.  Joy spread
through the world like the smell of pot at a Grateful Dead concert.

Tyler wanted to run ProtDist.pm from two simultaneous scripts with
the same working directory.  Jason pointed out that phylip doesn't
let you change the output filename.  He committed a hack^Wfix to
CVS.

Philip Lijnzaad reported a bug in BioPerl 1.0.2, which Hilmar reported
fixed for 1.2.

Paul Boutros continued to try and track down a bug with the LocusLink
IO code.  Allen Day opined it was a \r\n problem.

** Answered Questions

Scott Cain asked how to create an empty Bio::Seq object once you know
its length.  Hilmar replied that you can do this with 1.1.1 or later.

Charles Hauser asked how to trick Bio::SearchIO into thinking a
tab-delimited blast data file was a blast report, to extract accession
and description from the subj_name field.  Mathieu replied suggesting
simply ripping the description header parser code from the module
might be easier.

James Wasmuth asked how to write an alignment into a string instead of
a stream.  Ewan pointed him to IO::String, and Jason even supplied
code.

Nat Goodman asked what speedbumps people faced with BioPerl.  Rob
Edwards sent in an excellent list: lack of standardized names,
unobvious return values, the ease with which you can call an undefined
method while parsing genBank files, and the overwhelming amount of
What's In There.  Ewan replied suggesting a Lazy Programmer's Guide
to BioPerl.

Jason pointed Mike Pheasant toward Ensembl and
Bio::SeqFeatures::Gene::GeneStructure objects for help "merging exons
in all transcripts of a gene to come up with a new non-overlapping set
of start/end coordinates for all sequences that end up in any mRNA for
that gene" (whew!).

Eicke Felipe had a problem that turned out to be caused by mixing
1.0.2 and a later version.  

Yee Man asked whether Ewan would extend his protein Smith-Waterman
module to DNA.  Ewan replied that it's in the Wise2 package but
there's no XS bridge for it yet.  Yee volunteered to write said
bridge.  Yee also threw out this cool URL:
  http://poweredge.stanford.edu/BioinformaticsArchive/ClassicArticlesArchive/

Andy Nunberg why StandAloneBlast doesn't pick up BLASTDB envariable
changes.  Jason replied that it's set at 'use' time, not runtime and
showed 
  $Bio::Tools::Run::StandAloneBlast::DATADIR = '/localcopy';
as an alternative way to do it.

David Vilanova asked how to add subseqfeatures when reconstructing a
genbank annotation file.  Jason explained how the code and concepts
have changed (and showed sample code) and ended with a plea: "It would
be nice if someone would map the SeqFeature::Gene::GeneStructureI
objects into something similar to the below structure for direct
output by the SeqIO objects."

Renata Melo asked for information about using Smith-Waterman using DSM
with MPI or other parallel tools.  Aarom Mackey pointed to sesarch34
from the fasta distribution which has PVM and MPI implementations.