Removing children in a GFF

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Removing children in a GFF

Surya Saha
Hi Scott et al.,

Are there any tools/scripts to remove all the child features given a parent from a GFF file? For e.g., given a gene, it should remove all mRNAs, exons, CDSs and other child features. Some of this can be achieved via simple grep/sed but a more elegant method will be desirable. Thanks

-Surya

--

Surya Saha
Department of Plant Pathology, 
Cornell University, NY, USA.
Sol Genomics Network, 
Boyce Thompson Institute, Ithaca, NY, USA.

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Re: Removing children in a GFF

Scott Cain
Hi Surya,

I was waiting hoping somebody else would suggest something (since I wasn't aware of anything), but that seems to have turned up empty.  Just out of curiosity, why do you want to do that?

Scott



On Wed, Dec 11, 2013 at 11:13 PM, Surya Saha <[hidden email]> wrote:
Hi Scott et al.,

Are there any tools/scripts to remove all the child features given a parent from a GFF file? For e.g., given a gene, it should remove all mRNAs, exons, CDSs and other child features. Some of this can be achieved via simple grep/sed but a more elegant method will be desirable. Thanks

-Surya

--

Surya Saha
Department of Plant Pathology, 
Cornell University, NY, USA.
Sol Genomics Network, 
Boyce Thompson Institute, Ithaca, NY, USA.

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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Removing children in a GFF

Surya Saha
Hi Scott,

I am cleaning annotations for a genome and want to remove children of parent features that are now invalid. I went ahead and added the code myself since its simple enough with Bio::GFF3::LowLevel::Parser courtesy Rob B.

-Surya


On Wed, Dec 18, 2013 at 12:32 AM, Scott Cain <[hidden email]> wrote:
Hi Surya,

I was waiting hoping somebody else would suggest something (since I wasn't aware of anything), but that seems to have turned up empty.  Just out of curiosity, why do you want to do that?

Scott



On Wed, Dec 11, 2013 at 11:13 PM, Surya Saha <[hidden email]> wrote:
Hi Scott et al.,

Are there any tools/scripts to remove all the child features given a parent from a GFF file? For e.g., given a gene, it should remove all mRNAs, exons, CDSs and other child features. Some of this can be achieved via simple grep/sed but a more elegant method will be desirable. Thanks

-Surya

--

Surya Saha
Department of Plant Pathology, 
Cornell University, NY, USA.
Sol Genomics Network, 
Boyce Thompson Institute, Ithaca, NY, USA.

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Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--

Surya Saha
Department of Plant Pathology, 
Cornell University, NY, USA.
Sol Genomics Network, 
Boyce Thompson Institute, Ithaca, NY, USA.

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Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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