christmas_arrow glyph

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christmas_arrow glyph

Benjamin Hitz

Is this glyph supposed to be directed?, i.e,. the arrow should point in the direction of the $f->strand?
It does not appear to be in our gbrowse2 (2.17bugfix), and peering at source code it seems that it doen't even try...

Ben
--
Ben Hitz
Senior Scientific Programmer
Saccharomyces Genome Project
Stanford University
[hidden email]




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Re: christmas_arrow glyph

Scott Cain
Hi Ben,

The christmas_arrow glyph is a little strange, as it was contributed
by someone "outside" of the core BioGraphics developers (that is,
Lincoln didn't write it :-)  Nevertheless, I get stranded behavior
(see attached picture) when I modify the "yeast_simple" dataset that
comes with GBrowse to make the Genes track look like this:

[Genes]
feature      = gene
glyph        = christmas_arrow
stranded     = 1
bgcolor      = yellow
forwardcolor = yellow
reversecolor = turquoise
label        = sub { my $f = shift;
                     my $name = $f->display_name;
                     my @aliases = sort $f->attributes('Alias');
                     $name .= " (@aliases)" if @aliases;
                     $name;
  }
height       = 25
description  = 0
bump         = 2
key          = Named gene

In addition to changing the glyph, I added the stranded option and
bumped up the height.

Scott


On Wed, Feb 2, 2011 at 6:03 PM, Benjamin Hitz <[hidden email]> wrote:

>
> Is this glyph supposed to be directed?, i.e,. the arrow should point in the direction of the $f->strand?
> It does not appear to be in our gbrowse2 (2.17bugfix), and peering at source code it seems that it doen't even try...
>
> Ben
> --
> Ben Hitz
> Senior Scientific Programmer
> Saccharomyces Genome Project
> Stanford University
> [hidden email]
>
>
>
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Finally, a world-class log management solution at an even better price-free!
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February 28th, so secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsight-sfd2d
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Picture 2.png (9K) Download Attachment
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Re: christmas_arrow glyph

Benjamin Hitz

Hmmmm... that's what I have but Bio::Graphics version 2.12 not more recent.  I'll do some tests.

Ben
On Feb 3, 2011, at 7:24 AM, Scott Cain wrote:

> Hi Ben,
>
> The christmas_arrow glyph is a little strange, as it was contributed
> by someone "outside" of the core BioGraphics developers (that is,
> Lincoln didn't write it :-)  Nevertheless, I get stranded behavior
> (see attached picture) when I modify the "yeast_simple" dataset that
> comes with GBrowse to make the Genes track look like this:
>
> [Genes]
> feature      = gene
> glyph        = christmas_arrow
> stranded     = 1
> bgcolor      = yellow
> forwardcolor = yellow
> reversecolor = turquoise
> label        = sub { my $f = shift;
>                     my $name = $f->display_name;
>                     my @aliases = sort $f->attributes('Alias');
>                     $name .= " (@aliases)" if @aliases;
>                     $name;
>  }
> height       = 25
> description  = 0
> bump         = 2
> key          = Named gene
>
> In addition to changing the glyph, I added the stranded option and
> bumped up the height.
>
> Scott
>
>
> On Wed, Feb 2, 2011 at 6:03 PM, Benjamin Hitz <[hidden email]> wrote:
>>
>> Is this glyph supposed to be directed?, i.e,. the arrow should point in the direction of the $f->strand?
>> It does not appear to be in our gbrowse2 (2.17bugfix), and peering at source code it seems that it doen't even try...
>>
>> Ben
>> --
>> Ben Hitz
>> Senior Scientific Programmer
>> Saccharomyces Genome Project
>> Stanford University
>> [hidden email]
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
>> Finally, a world-class log management solution at an even better price-free!
>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> February 28th, so secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsight-sfd2d
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> <Picture 2.png>

--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** [hidden email]




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