[Bioperl-l] somethin' strange about RootI

Jason Stajich jason@chg.mc.duke.edu
Sat, 2 Dec 2000 10:14:26 -0500 (EST)

There are some funky things going on with
translate and the can_call_new routine I believe.
I have not been able to pinpoint what specifically is happening but I have
seen this on a UNIX box as well.  I'll make sure some variant of the below
code makes it into the tests.

The next few weeks the bioperl code is going to be in transition and we're
going to try really hard to check in code that works, and pass all the
tests, but bugs happen.

Volunteers for more tests writing are definitely welcome if you don't want
to get into the code rewrite fray.

On Fri, 1 Dec 2000, Mark Wilkinson wrote:

> Hi Group,
> Is there something about the RootI that has changed to prevent these
> lines from
> working properly? (This routine was working until I cvs-updated my
> bioperl "live" folder this afternoon...)
> my $SelectedSeq = Bio::PrimarySeq->new(-seq => (join '',@SelectedSeqs),
> -moltype => 'dna');
> my $SelectedTrans = $SelectedSeq->translate()->seq;
> I get the following error (in both Windows and Linux):
> -------------------- EXCEPTION --------------------
> MSG:
> SCRIPT: Workbench2.pl
> Bio::Root::RootI::new(82)
> Bio::PrimarySeqI::translate(602)
> QueryScreen::_checkFrame(286)
> QueryScreen::__ANON__(242)
> Tk::MainLoop(329)
> QueryScreen::new(581)
> main::Workbench2.pl(18)
> ---------------------------------------------------
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Jason Stajich
Center for Human Genetics
Duke University Medical Center