[Genquire-users] Ugly bug introduced last week and now fixed

[Mark Wilkinson]

Hi All,

I owe you a beer :-)  While fixing the de novo feature creation last
week I managed to introduce another bug which prevented the sequence
from being properly displayed on the minus strand.  As a consequence,
the coordinates (i.e. feature locations) of any de novo features on the
minus strand are also buggered.  Worse yet, the ones on the plus strand
have an off by one in their length (correct start, length too long).

Other annoyances appeared while fixing this bug, and I have made some
other changes.  Now, by default, *all* features are displayed in the
nucleotide view when pressing the "c" key on the canvas (previously it
was just the exons).  I thought this was more intuitive, as it took me a
while to figure out that the fact that I couldn't see my newly created
things was not a Genquire bug, but a Genquire feature ;-)  I was
subsequently annoyed and decided I didn't like that "feature" so I
changed it.  I also discovered that it choked if you had only non-exon
type features selected and asked for the ShowSequence spliced ("s").
This is also fixed now.

I did notice something peculiar, which perhaps Dave can answer better
than I can...??  The Feature::mod module expects the strand information
to be given to it in GFF format, rather than in BioPerl format as is the
case for other Feature::objects.  i.e. use the +/- strand designation,
instead of the 1/-1 designation normally used in BioPerl.  If you don't,
then Feature::mod appends a "1" to the end of the strand information,
and you can end up with ->strand = -11  ... which isn't any good to
anybody is it unless we are working with an unusual DNA type that has 22
strands  :-)

Anyway, as far as I can tell it is all fixed up and working again.

Sorry about the fuss and commotion.  I didn't notice it until I went
through a detailed series of feature creations today for my colleague
and discovered that they were all off by one!  Ack!

Cheers all,

M


--
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"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada