[Bioperl-l] Bio::Graphics - several

Alper Yilmaz alperyilmaz at gmail.com
Mon Jul 14 17:34:26 EDT 2008


Hi,
I have couple questions about Bio::Graphics.
a- even though I played around with start, end, width, length values,
I wasn't able to make a ruler which starts from -1600 and ends at 0
(promoter region). How can I make a ruler, which has negative values
and decreases towards right?
In such a case, what happens to start and end values of the box
glyphs? How can I adjust start and end values of an element located at
1500bp so that it's shown at -100bp, in other words are negative
values taken as is or interpreted as "less than start" ?

b- some of the recognized variables for  -link argument are $name, $id, etc.
$name corresponds to -display_name of Bio::SeqFeature::Generic.What
does $id correspond to? I tried to assign value to $id but it was not
successful
   -link=>    sub {
			my $element = shift;
			my $id = $element->seq_id;
			return 'http://database/address.html?promoter_id=$id';
			},
In this statement even if I try to print $id within sub, it does not
print anything.

c- I didn't come accross any scripts or tutorials about including pan
or zoom button (as in GBrowser). How can I add those functionalities
to already available graphics generated by Bio::Graphics ?


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