[Gmod-ajax] New version of FeatureSequence

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[Gmod-ajax] New version of FeatureSequence

Saari, Travis

I’ve added some new functionality to the FeatureSequence plugin, which some of you may be interested in:

 

The plugin previously had problems with the way that GFF3’s are commonly structured – that is, overlapping regions of ‘exon’ and ‘CDS’ would cause problems. It now has a method to follow GFF3 specification for this common type of feature. Implicitly defined UTR’s in this way are also explicitly defined for the plugin, so that they can be manipulated as a group.

 

Also, the plugin now has a way to handle three-leveled features (e.g. gene -> mRNA -> CDS). The plugin will detect a three-leveled feature and prompt the user to select a particular transcript before opening the FeatureSequence dialog.

 

This functionality was important for my own work, and I know that several of you have requested similar things as well. I hope that you all can try it out and let me know how it works for you.

 

Best,

 

 

Travis Saari


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Re: New version of FeatureSequence

Scott Cain
Hi Travis,

Thanks so much for this.  Question: what branch git branch are these changes on? When I just did a simple pull on the "develop" branche, jbrowse crashed because it required dijit/Layout/LayoutContainer and ContentPane and those aren't included in the JBrowse source.  I switched to the master branch and it runs but with the warning message dialog that I would think would go away with your described changes.  I also noticed there are new tags for 1.1 and 1.2, but you didn't mention those in your email, so I'm not sure what to do with those either.

Thanks,
Scott


On Mon, Sep 12, 2016 at 11:10 AM, Saari, Travis <[hidden email]> wrote:

I’ve added some new functionality to the FeatureSequence plugin, which some of you may be interested in:

 

The plugin previously had problems with the way that GFF3’s are commonly structured – that is, overlapping regions of ‘exon’ and ‘CDS’ would cause problems. It now has a method to follow GFF3 specification for this common type of feature. Implicitly defined UTR’s in this way are also explicitly defined for the plugin, so that they can be manipulated as a group.

 

Also, the plugin now has a way to handle three-leveled features (e.g. gene -> mRNA -> CDS). The plugin will detect a three-leveled feature and prompt the user to select a particular transcript before opening the FeatureSequence dialog.

 

This functionality was important for my own work, and I know that several of you have requested similar things as well. I hope that you all can try it out and let me know how it works for you.

 

Best,

 

 

Travis Saari


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
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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

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
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Re: New version of FeatureSequence

Keiran Raine
Hi Scott,

Do you mean the branch of the plugin repo or JBrowse itself?  It seems to be working for me with:

cd JBrowse/plugins
rm -rf FeatureSequence

.. and adding the relevant bit to the conf and track defenitions as in the repo docs (https://github.com/tsaari88/FeatureSequence/tree/master#to-use-the-featuresequence-plugin).


Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 12 Sep 2016, at 19:13, Scott Cain <[hidden email]> wrote:

Hi Travis,

Thanks so much for this.  Question: what branch git branch are these changes on? When I just did a simple pull on the "develop" branche, jbrowse crashed because it required dijit/Layout/LayoutContainer and ContentPane and those aren't included in the JBrowse source.  I switched to the master branch and it runs but with the warning message dialog that I would think would go away with your described changes.  I also noticed there are new tags for 1.1 and 1.2, but you didn't mention those in your email, so I'm not sure what to do with those either.

Thanks,
Scott


On Mon, Sep 12, 2016 at 11:10 AM, Saari, Travis <[hidden email]> wrote:

I’ve added some new functionality to the FeatureSequence plugin, which some of you may be interested in:

 

The plugin previously had problems with the way that GFF3’s are commonly structured – that is, overlapping regions of ‘exon’ and ‘CDS’ would cause problems. It now has a method to follow GFF3 specification for this common type of feature. Implicitly defined UTR’s in this way are also explicitly defined for the plugin, so that they can be manipulated as a group.

 

Also, the plugin now has a way to handle three-leveled features (e.g. gene -> mRNA -> CDS). The plugin will detect a three-leveled feature and prompt the user to select a particular transcript before opening the FeatureSequence dialog.

 

This functionality was important for my own work, and I know that several of you have requested similar things as well. I hope that you all can try it out and let me know how it works for you.

 

Best,

 

 

Travis Saari


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
_______________________________________________
Gmod-ajax mailing list
[hidden email]
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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
------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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