suppress child features

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suppress child features

Kenlee Nakasugi-2
Hi,

Is there a way to suppress the children features of a parent in a GFF?

E.g. say in the GFF there is the parent Gene, then the children are mRNA, exon, CDS etc
Is there a way to suppress mRNA, exon, CDS by the Track stanza, maybe based on the "Type" field?

Cheers
Ken

--------------------

Kenlee Nakasugi

Rm873, Bldg-G08 (level 8)
School of Molecular Bioscience
University of New South Wales
Ph: 02-9114-1321
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Re: suppress child features

Timothy Parnell
Hi Kenlee,

Whenever I want to suppress sub features (exons, etc), for example, going from a detailed view zoomed in and a generic view when zoomed out, I switch the glyph from gene to box using semantic zoom.

[Genes]
feature = gene
glyph = gene
etc

[Genes:100000]
glyph = box
stranded = 1
label = 0

Hope that helps.
Tim

On Nov 6, 2013, at 4:44 PM, Kenlee Nakasugi <[hidden email]> wrote:

> Hi,
>
> Is there a way to suppress the children features of a parent in a GFF?
>
> E.g. say in the GFF there is the parent Gene, then the children are mRNA, exon, CDS etc
> Is there a way to suppress mRNA, exon, CDS by the Track stanza, maybe based on the "Type" field?
>
> Cheers
> Ken
>
> --------------------
>
> Kenlee Nakasugi
>
> Rm873, Bldg-G08 (level 8)
> School of Molecular Bioscience
> University of New South Wales
> Ph: 02-9114-1321
> ------------------------------------------------------------------------------
> November Webinars for C, C++, Fortran Developers
> Accelerate application performance with scalable programming models. Explore
> techniques for threading, error checking, porting, and tuning. Get the most
> from the latest Intel processors and coprocessors. See abstracts and register
> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
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Re: suppress child features

Scott Cain
In reply to this post by Kenlee Nakasugi-2
Hi Ken,

All glyphs support an option called "ignore_sub_part" where you supply the feature types to ignore.  Alternatively, like Tim suggested, if you just want a block that covers the whole gene, just use the generic glyph.

Scott



On Wed, Nov 6, 2013 at 6:44 PM, Kenlee Nakasugi <[hidden email]> wrote:
Hi,

Is there a way to suppress the children features of a parent in a GFF?

E.g. say in the GFF there is the parent Gene, then the children are mRNA, exon, CDS etc
Is there a way to suppress mRNA, exon, CDS by the Track stanza, maybe based on the "Type" field?

Cheers
Ken

--------------------

Kenlee Nakasugi

Rm873, Bldg-G08 (level 8)
School of Molecular Bioscience
University of New South Wales
Ph: 02-9114-1321
------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
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--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
November Webinars for C, C++, Fortran Developers
Accelerate application performance with scalable programming models. Explore
techniques for threading, error checking, porting, and tuning. Get the most
from the latest Intel processors and coprocessors. See abstracts and register
http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk
_______________________________________________
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