[Bioperl-l] Re: Bio::Graphics - several

Siddhartha Basu sidd.basu at gmail.com
Wed Jul 16 10:37:06 EDT 2008


On Mon, 14 Jul 2008, Alper Yilmaz wrote:

> 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?

This post might answer your question ....


> 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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