[Bioperl-l] Bio::Location::Simple

[David Block]

Okay, I've had my head stuck in Workbench among other things, but I
thought I'd test Workbench against bioperl-live to see where things were
at.

Bad.

The Blast module still calls Bio::Root::Err, which has a problem with
"std" - here is the printout.

[dblock@exon Workbench2]$ perl Workbench2.pl 
"std" is not defined in %Bio::Root::Object::EXPORT_TAGS at
/home/dblock/work/bioperl/bioperl-live/Bio/Root/Err.pm line 22
Can't continue after import errors at
/home/dblock/work/bioperl/bioperl-live/Bio/Root/Err.pm line 22
BEGIN failed--compilation aborted at
/home/dblock/work/bioperl/bioperl-live/Bio/Root/Err.pm line 22.
BEGIN failed--compilation aborted at
/home/dblock/work/bioperl/bioperl-live/Bio/Root/RootI.pm line 64.
BEGIN failed--compilation aborted at
/home/dblock/work/bioperl/bioperl-live/Bio/Root/Object.pm line 24.
BEGIN failed--compilation aborted at
/home/dblock/work/bioperl/bioperl-live/Bio/Tools/SeqAnal.pm line 15.
BEGIN failed--compilation aborted at
/home/dblock/work/bioperl/bioperl-live/Bio/Tools/Blast.pm line 25.
BEGIN failed--compilation aborted at Utilities.pm line 5.
BEGIN failed--compilation aborted at QueryScreen.pm line 6.
BEGIN failed--compilation aborted at Workbench2.pl line 13.

Fine, ignore Blast.pm, we'll replace it with BPlite.  But then,

[dblock@exon Workbench2]$ perl Workbench2.pl 
Can't locate Bio/Location/Simple.pm in @INC (@INC
contains: /home/dblock/work/bioperl/bioperl-gui
/home/dblock/work/bioperl/bioperl-live /home/dblock/lib/perl5
/usr/lib/perl5/5.00503/i386-linux /usr/lib/perl5/5.00503
/usr/lib/perl5/site_perl/5.005/i386-linux /usr/lib/perl5/site_perl/5.005
.) at /home/dblock/work/bioperl/bioperl-live/Bio/SeqFeature/Generic.pm
line 122.
BEGIN failed--compilation aborted at
/home/dblock/work/bioperl/bioperl-live/Bio/SeqFeature/Generic.pm line 122.
BEGIN failed--compilation aborted at
/home/dblock/work/bioperl/bioperl-live/Bio/SeqFeature/FeaturePair.pm line
96.
BEGIN failed--compilation aborted at
/home/dblock/work/bioperl/bioperl-live/Bio/Tools/Sim4/Exon.pm line 100.
BEGIN failed--compilation aborted at
/home/dblock/work/bioperl/bioperl-live/Bio/Tools/Sim4/Results.pm line 127.
BEGIN failed--compilation aborted at WB_Sim4.pm line 6.
BEGIN failed--compilation aborted at QueryScreen.pm line 20.
BEGIN failed--compilation aborted at Workbench2.pl line 13.

So there is no implementation of Bio::Location::Simple yet.  Is this the
thing that's supposed to return start/stop values?  Does someone have a
preliminary version?

I have a bit of time I can throw at bioperl now...

-- 
David Block
dblock@gene.pbi.nrc.ca
http://bioinfo.pbi.nrc.ca/dblock/wiki
Plant Biotechnology Institute
National Research Council of Canada
Saskatoon, Saskatchewan