[Gmod-ajax] Flip orientation

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[Gmod-ajax] Flip orientation

Scott Cain
Hi Ian and Eric,

We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:


Thanks,
Scott


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Re: Flip orientation

nathandunn

Colin had written one for doing reverses explicitly in JBrowse:


I’m sure it will need to be cleaned up a bit, but it had appeared to work when demoed.  

The one we’re developing for Apollo will do more (combining arbitrary scaffolds in any orientation), but our initially foray will require an Apollo login and won’t be out for at least a month.  

Nathan

On Jan 10, 2017, at 7:35 AM, Scott Cain <[hidden email]> wrote:

Hi Ian and Eric,

We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:


Thanks,
Scott


--
------------------------------------------------------------------------
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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Re: Flip orientation

Scott Cain
Hi Nathan,

Thanks for pointing that out, though it doesn't seem to work at the moment.  I installed it in WormBase's staging server:


It doesn't reverse complement the current view, but does have the exciting effect of taking you to a seemingly random location in the same sequence you're currently viewing.  It will help with people wanting to discover new things! :-)  I suspect the "random" place is a mirror image location, reflecting around the center of the sequence and is a result of a blown sign somewhere.

Scott


On Tue, Jan 10, 2017 at 11:48 AM, Nathan Dunn <[hidden email]> wrote:

Colin had written one for doing reverses explicitly in JBrowse:


I’m sure it will need to be cleaned up a bit, but it had appeared to work when demoed.  

The one we’re developing for Apollo will do more (combining arbitrary scaffolds in any orientation), but our initially foray will require an Apollo login and won’t be out for at least a month.  

Nathan

On Jan 10, 2017, at 7:35 AM, Scott Cain <[hidden email]> wrote:

Hi Ian and Eric,

We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:


Thanks,
Scott


--
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Re: Flip orientation

Colin
Hi Scott,
I think the problem you observe with projectionplugin is because the trackList needs some editing first.

You have to need to edit the trackList.json to change the storeClass from JBrowse/Store/SeqFeature/Sequence to ProjectionPlugin/Store/SeqFeature/ReverseSequence, JBrowse/Store/SeqFeature/NCList to ProjectionPlugin/Store/SeqFeature/ReverseNCList, etc. The augmented storeClass implements the ability to do the reverse complement and can display non-reversed too.


-Colin

On Tue, Jan 10, 2017 at 12:22 PM, Scott Cain <[hidden email]> wrote:
Hi Nathan,

Thanks for pointing that out, though it doesn't seem to work at the moment.  I installed it in WormBase's staging server:


It doesn't reverse complement the current view, but does have the exciting effect of taking you to a seemingly random location in the same sequence you're currently viewing.  It will help with people wanting to discover new things! :-)  I suspect the "random" place is a mirror image location, reflecting around the center of the sequence and is a result of a blown sign somewhere.

Scott


On Tue, Jan 10, 2017 at 11:48 AM, Nathan Dunn <[hidden email]> wrote:

Colin had written one for doing reverses explicitly in JBrowse:


I’m sure it will need to be cleaned up a bit, but it had appeared to work when demoed.  

The one we’re developing for Apollo will do more (combining arbitrary scaffolds in any orientation), but our initially foray will require an Apollo login and won’t be out for at least a month.  

Nathan

On Jan 10, 2017, at 7:35 AM, Scott Cain <[hidden email]> wrote:

Hi Ian and Eric,

We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:


Thanks,
Scott


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Re: Flip orientation

Scott Cain
Ah, who actually reads documentation, amiright? :-)  OK, now I only have to modify the store class of about 1300 tracks.

On Tue, Jan 10, 2017 at 1:08 PM, Colin <[hidden email]> wrote:
Hi Scott,
I think the problem you observe with projectionplugin is because the trackList needs some editing first.

You have to need to edit the trackList.json to change the storeClass from JBrowse/Store/SeqFeature/Sequence to ProjectionPlugin/Store/SeqFeature/ReverseSequence, JBrowse/Store/SeqFeature/NCList to ProjectionPlugin/Store/SeqFeature/ReverseNCList, etc. The augmented storeClass implements the ability to do the reverse complement and can display non-reversed too.


-Colin

On Tue, Jan 10, 2017 at 12:22 PM, Scott Cain <[hidden email]> wrote:
Hi Nathan,

Thanks for pointing that out, though it doesn't seem to work at the moment.  I installed it in WormBase's staging server:


It doesn't reverse complement the current view, but does have the exciting effect of taking you to a seemingly random location in the same sequence you're currently viewing.  It will help with people wanting to discover new things! :-)  I suspect the "random" place is a mirror image location, reflecting around the center of the sequence and is a result of a blown sign somewhere.

Scott


On Tue, Jan 10, 2017 at 11:48 AM, Nathan Dunn <[hidden email]> wrote:

Colin had written one for doing reverses explicitly in JBrowse:


I’m sure it will need to be cleaned up a bit, but it had appeared to work when demoed.  

The one we’re developing for Apollo will do more (combining arbitrary scaffolds in any orientation), but our initially foray will require an Apollo login and won’t be out for at least a month.  

Nathan

On Jan 10, 2017, at 7:35 AM, Scott Cain <[hidden email]> wrote:

Hi Ian and Eric,

We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:


Thanks,
Scott


--
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GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
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Re: Flip orientation

nathandunn

Scott,

You can probably modify / fork the plugin to automatically do this for you.  


Of course, I’m not sure whether or not that would be more work for you. 

Nathan

On Jan 10, 2017, at 11:24 AM, Scott Cain <[hidden email]> wrote:

Ah, who actually reads documentation, amiright? :-)  OK, now I only have to modify the store class of about 1300 tracks.

On Tue, Jan 10, 2017 at 1:08 PM, Colin <[hidden email]> wrote:
Hi Scott,
I think the problem you observe with projectionplugin is because the trackList needs some editing first.

You have to need to edit the trackList.json to change the storeClass from JBrowse/Store/SeqFeature/Sequence to ProjectionPlugin/Store/SeqFeature/ReverseSequence, JBrowse/Store/SeqFeature/NCList to ProjectionPlugin/Store/SeqFeature/ReverseNCList, etc. The augmented storeClass implements the ability to do the reverse complement and can display non-reversed too.


-Colin

On Tue, Jan 10, 2017 at 12:22 PM, Scott Cain <[hidden email]> wrote:
Hi Nathan,

Thanks for pointing that out, though it doesn't seem to work at the moment.  I installed it in WormBase's staging server:


It doesn't reverse complement the current view, but does have the exciting effect of taking you to a seemingly random location in the same sequence you're currently viewing.  It will help with people wanting to discover new things! :-)  I suspect the "random" place is a mirror image location, reflecting around the center of the sequence and is a result of a blown sign somewhere.

Scott


On Tue, Jan 10, 2017 at 11:48 AM, Nathan Dunn <[hidden email]> wrote:

Colin had written one for doing reverses explicitly in JBrowse:


I’m sure it will need to be cleaned up a bit, but it had appeared to work when demoed.  

The one we’re developing for Apollo will do more (combining arbitrary scaffolds in any orientation), but our initially foray will require an Apollo login and won’t be out for at least a month.  

Nathan

On Jan 10, 2017, at 7:35 AM, Scott Cain <[hidden email]> wrote:

Hi Ian and Eric,

We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:


Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank" class="">216-392-3087
Ontario Institute for Cancer Research
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--
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Re: Flip orientation

Scott Cain
Hi Colin and Nathan,

So it sort of works but is not quite there in a few ways.  See the attached to images.  I'll leave this in place for a while (it's a few weeks before the next release):

http://staging.wormbase.org/tools/genome/jbrowse-simple/full.html?data=data%2Fc_elegans_PRJNA13758&loc=III%3A13699453..13732152&tracks=Curated_Genes&highlight=

1. I updated the storeClass in both the Curated Genes track and the DNA track (to plugins/projectionplugin/js/Store/SeqFeature/SequenceChunks) selecting "reverse complement" still makes it look like I've jumped to somewhere else in the genome (note the coordinates at the top of each image).  I think those are the same features, but I can't tell because:

2. All of the labels get lost.  In this instance, the labels are from js callbacks in the config and they probably aren't getting evaluated again, or aren't get evaluated correctly.

3. Along those lines, the color attribute callback is getting evaluated but is not getting it right either.  The color shouldn't change when I flip directions (the genes are colored by strand).  Even if I flip the orientation, the strand of the feature doesn't change.  Additionally, not shown in these images but I noticed elsewhere that non-coding genes are supposed to be gray no matter what, but when I flip, they get colored according to strand like the coding genes.  I suspect there may be a way to fix this by rewriting the callbacks that do this, but that's the sort of thing that might effect other things to, so I/we will need to be on the look out for them.  In this instance, the script needs to be able to detect that it is flipped and so return the opposite colors from what it would normally do.

4. The glyphs are also a little wonky in terms of spacing between transcripts is off and they are smooshed together (that's the technical term).

I don't really have the time to devote to this right now, but perhaps after PAG I can poke around a little bit.  If anybody wants to before then, I'll be grateful :-)

Thanks,
Scott


On Tue, Jan 10, 2017 at 2:25 PM, Nathan Dunn <[hidden email]> wrote:

>
>
> Scott,
>
> You can probably modify / fork the plugin to automatically do this for you.  
>
> https://github.com/GMOD/Apollo/blob/master/client/apollo/js/TrackConfigTransformer.js#L26
>
> Of course, I’m not sure whether or not that would be more work for you.
>
> Nathan
>
> On Jan 10, 2017, at 11:24 AM, Scott Cain <[hidden email]> wrote:
>
> Ah, who actually reads documentation, amiright? :-)  OK, now I only have to modify the store class of about 1300 tracks.
>
> On Tue, Jan 10, 2017 at 1:08 PM, Colin <[hidden email]> wrote:
>>
>> Hi Scott,
>> I think the problem you observe with projectionplugin is because the trackList needs some editing first.
>>
>> You have to need to edit the trackList.json to change the storeClass from JBrowse/Store/SeqFeature/Sequence to ProjectionPlugin/Store/SeqFeature/ReverseSequence, JBrowse/Store/SeqFeature/NCList to ProjectionPlugin/Store/SeqFeature/ReverseNCList, etc. The augmented storeClass implements the ability to do the reverse complement and can display non-reversed too.
>>
>>
>> -Colin
>>
>> On Tue, Jan 10, 2017 at 12:22 PM, Scott Cain <[hidden email]> wrote:
>>>
>>> Hi Nathan,
>>>
>>> Thanks for pointing that out, though it doesn't seem to work at the moment.  I installed it in WormBase's staging server:
>>>
>>> http://staging.wormbase.org/tools/genome/jbrowse-simple/full.html?data=data%2Fc_elegans_PRJNA13758&loc=MtDNA%3A9561..13794&tracks=Classical_alleles%2CPolymorphisms%2CCurated_Genes&highlight=
>>>
>>> It doesn't reverse complement the current view, but does have the exciting effect of taking you to a seemingly random location in the same sequence you're currently viewing.  It will help with people wanting to discover new things! :-)  I suspect the "random" place is a mirror image location, reflecting around the center of the sequence and is a result of a blown sign somewhere.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jan 10, 2017 at 11:48 AM, Nathan Dunn <[hidden email]> wrote:
>>>>
>>>>
>>>> Colin had written one for doing reverses explicitly in JBrowse:
>>>>
>>>> https://github.com/elsiklab/projectionplugin
>>>>
>>>> I’m sure it will need to be cleaned up a bit, but it had appeared to work when demoed.  
>>>>
>>>> The one we’re developing for Apollo will do more (combining arbitrary scaffolds in any orientation), but our initially foray will require an Apollo login and won’t be out for at least a month.  
>>>>
>>>> Nathan
>>>>
>>>> On Jan 10, 2017, at 7:35 AM, Scott Cain <[hidden email]> wrote:
>>>>
>>>> Hi Ian and Eric,
>>>>
>>>> We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:
>>>>
>>>> https://github.com/GMOD/jbrowse/issues/170
>>>>
>>>> Thanks,
>>>> Scott
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>> ------------------------------------------------------------------------------
>>>> Developer Access Program for Intel Xeon Phi Processors
>>>> Access to Intel Xeon Phi processor-based developer platforms.
>>>> With one year of Intel Parallel Studio XE.
>>>> Training and support from Colfax.
>>>> Order your platform today. http://sdm.link/xeonphi_______________________________________________
>>>> Gmod-ajax mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>> ------------------------------------------------------------------------------
>>> Developer Access Program for Intel Xeon Phi Processors
>>> Access to Intel Xeon Phi processor-based developer platforms.
>>> With one year of Intel Parallel Studio XE.
>>> Training and support from Colfax.
>>> Order your platform today. http://sdm.link/xeonphi
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> 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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Ontario Institute for Cancer Research

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Re: Flip orientation

Suzanna Lewis-3
In reply to this post by nathandunn
Nathan, Ian and Eric

Forgive me, but isn't reverse-complement already working? (It's the same as "flip"). Is this a problem with core/essential/key fixes being made in Apollo, but not finding there way back into JBrowse.

It's very frustrating. I've been hammering on this for years now. I cannot emphasize enough how important this is. Will there ever be a day that dawns when it's done?

-S


On Tue, Jan 10, 2017 at 8:48 AM, Nathan Dunn <[hidden email]> wrote:

Colin had written one for doing reverses explicitly in JBrowse:


I’m sure it will need to be cleaned up a bit, but it had appeared to work when demoed.  

The one we’re developing for Apollo will do more (combining arbitrary scaffolds in any orientation), but our initially foray will require an Apollo login and won’t be out for at least a month.  

Nathan

On Jan 10, 2017, at 7:35 AM, Scott Cain <[hidden email]> wrote:

Hi Ian and Eric,

We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:


Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
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Re: Flip orientation

Monica Munoz-Torres
In reply to this post by Scott Cain
Dear Scott, 

I offer a suggestion: have a cup'o tea and wait a little more until we issue our release with updates on transformation of coordinates before investing more of your time down this path. We are nearly there. ;)

cheers, 
~moni.

-- 
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720


On Tue, Jan 10, 2017 at 12:56 PM, Scott Cain <[hidden email]> wrote:
Hi Colin and Nathan,

So it sort of works but is not quite there in a few ways.  See the attached to images.  I'll leave this in place for a while (it's a few weeks before the next release):

http://staging.wormbase.org/tools/genome/jbrowse-simple/full.html?data=data%2Fc_elegans_PRJNA13758&loc=III%3A13699453..13732152&tracks=Curated_Genes&highlight=

1. I updated the storeClass in both the Curated Genes track and the DNA track (to plugins/projectionplugin/js/Store/SeqFeature/SequenceChunks) selecting "reverse complement" still makes it look like I've jumped to somewhere else in the genome (note the coordinates at the top of each image).  I think those are the same features, but I can't tell because:

2. All of the labels get lost.  In this instance, the labels are from js callbacks in the config and they probably aren't getting evaluated again, or aren't get evaluated correctly.

3. Along those lines, the color attribute callback is getting evaluated but is not getting it right either.  The color shouldn't change when I flip directions (the genes are colored by strand).  Even if I flip the orientation, the strand of the feature doesn't change.  Additionally, not shown in these images but I noticed elsewhere that non-coding genes are supposed to be gray no matter what, but when I flip, they get colored according to strand like the coding genes.  I suspect there may be a way to fix this by rewriting the callbacks that do this, but that's the sort of thing that might effect other things to, so I/we will need to be on the look out for them.  In this instance, the script needs to be able to detect that it is flipped and so return the opposite colors from what it would normally do.

4. The glyphs are also a little wonky in terms of spacing between transcripts is off and they are smooshed together (that's the technical term).

I don't really have the time to devote to this right now, but perhaps after PAG I can poke around a little bit.  If anybody wants to before then, I'll be grateful :-)

Thanks,
Scott


On Tue, Jan 10, 2017 at 2:25 PM, Nathan Dunn <[hidden email]> wrote:

>
>
> Scott,
>
> You can probably modify / fork the plugin to automatically do this for you.  
>
> https://github.com/GMOD/Apollo/blob/master/client/apollo/js/TrackConfigTransformer.js#L26
>
> Of course, I’m not sure whether or not that would be more work for you.
>
> Nathan
>
> On Jan 10, 2017, at 11:24 AM, Scott Cain <[hidden email]> wrote:
>
> Ah, who actually reads documentation, amiright? :-)  OK, now I only have to modify the store class of about 1300 tracks.
>
> On Tue, Jan 10, 2017 at 1:08 PM, Colin <[hidden email]> wrote:
>>
>> Hi Scott,
>> I think the problem you observe with projectionplugin is because the trackList needs some editing first.
>>
>> You have to need to edit the trackList.json to change the storeClass from JBrowse/Store/SeqFeature/Sequence to ProjectionPlugin/Store/SeqFeature/ReverseSequence, JBrowse/Store/SeqFeature/NCList to ProjectionPlugin/Store/SeqFeature/ReverseNCList, etc. The augmented storeClass implements the ability to do the reverse complement and can display non-reversed too.
>>
>>
>> -Colin
>>
>> On Tue, Jan 10, 2017 at 12:22 PM, Scott Cain <[hidden email]> wrote:
>>>
>>> Hi Nathan,
>>>
>>> Thanks for pointing that out, though it doesn't seem to work at the moment.  I installed it in WormBase's staging server:
>>>
>>> http://staging.wormbase.org/tools/genome/jbrowse-simple/full.html?data=data%2Fc_elegans_PRJNA13758&loc=MtDNA%3A9561..13794&tracks=Classical_alleles%2CPolymorphisms%2CCurated_Genes&highlight=
>>>
>>> It doesn't reverse complement the current view, but does have the exciting effect of taking you to a seemingly random location in the same sequence you're currently viewing.  It will help with people wanting to discover new things! :-)  I suspect the "random" place is a mirror image location, reflecting around the center of the sequence and is a result of a blown sign somewhere.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jan 10, 2017 at 11:48 AM, Nathan Dunn <[hidden email]> wrote:
>>>>
>>>>
>>>> Colin had written one for doing reverses explicitly in JBrowse:
>>>>
>>>> https://github.com/elsiklab/projectionplugin
>>>>
>>>> I’m sure it will need to be cleaned up a bit, but it had appeared to work when demoed.  
>>>>
>>>> The one we’re developing for Apollo will do more (combining arbitrary scaffolds in any orientation), but our initially foray will require an Apollo login and won’t be out for at least a month.  
>>>>
>>>> Nathan
>>>>
>>>> On Jan 10, 2017, at 7:35 AM, Scott Cain <[hidden email]> wrote:
>>>>
>>>> Hi Ian and Eric,
>>>>
>>>> We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:
>>>>
>>>> https://github.com/GMOD/jbrowse/issues/170
>>>>
>>>> Thanks,
>>>> Scott
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
>>>> Ontario Institute for Cancer Research
>>>> ------------------------------------------------------------------------------
>>>> Developer Access Program for Intel Xeon Phi Processors
>>>> Access to Intel Xeon Phi processor-based developer platforms.
>>>> With one year of Intel Parallel Studio XE.
>>>> Training and support from Colfax.
>>>> Order your platform today. http://sdm.link/xeonphi_______________________________________________
>>>> Gmod-ajax mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>> ------------------------------------------------------------------------------
>>> Developer Access Program for Intel Xeon Phi Processors
>>> Access to Intel Xeon Phi processor-based developer platforms.
>>> With one year of Intel Parallel Studio XE.
>>> Training and support from Colfax.
>>> Order your platform today. http://sdm.link/xeonphi
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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Re: Flip orientation

Scott Cain
I'm good with waiting :-)  The PI who asked about it on the other hand...  (Kidding, I can feign progress while I wait :-)



On Tue, Jan 10, 2017 at 4:11 PM, Monica Munoz-Torres <[hidden email]> wrote:
Dear Scott, 

I offer a suggestion: have a cup'o tea and wait a little more until we issue our release with updates on transformation of coordinates before investing more of your time down this path. We are nearly there. ;)

cheers, 
~moni.

-- 
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720


On Tue, Jan 10, 2017 at 12:56 PM, Scott Cain <[hidden email]> wrote:
Hi Colin and Nathan,

So it sort of works but is not quite there in a few ways.  See the attached to images.  I'll leave this in place for a while (it's a few weeks before the next release):

http://staging.wormbase.org/tools/genome/jbrowse-simple/full.html?data=data%2Fc_elegans_PRJNA13758&loc=III%3A13699453..13732152&tracks=Curated_Genes&highlight=

1. I updated the storeClass in both the Curated Genes track and the DNA track (to plugins/projectionplugin/js/Store/SeqFeature/SequenceChunks) selecting "reverse complement" still makes it look like I've jumped to somewhere else in the genome (note the coordinates at the top of each image).  I think those are the same features, but I can't tell because:

2. All of the labels get lost.  In this instance, the labels are from js callbacks in the config and they probably aren't getting evaluated again, or aren't get evaluated correctly.

3. Along those lines, the color attribute callback is getting evaluated but is not getting it right either.  The color shouldn't change when I flip directions (the genes are colored by strand).  Even if I flip the orientation, the strand of the feature doesn't change.  Additionally, not shown in these images but I noticed elsewhere that non-coding genes are supposed to be gray no matter what, but when I flip, they get colored according to strand like the coding genes.  I suspect there may be a way to fix this by rewriting the callbacks that do this, but that's the sort of thing that might effect other things to, so I/we will need to be on the look out for them.  In this instance, the script needs to be able to detect that it is flipped and so return the opposite colors from what it would normally do.

4. The glyphs are also a little wonky in terms of spacing between transcripts is off and they are smooshed together (that's the technical term).

I don't really have the time to devote to this right now, but perhaps after PAG I can poke around a little bit.  If anybody wants to before then, I'll be grateful :-)

Thanks,
Scott


On Tue, Jan 10, 2017 at 2:25 PM, Nathan Dunn <[hidden email]> wrote:

>
>
> Scott,
>
> You can probably modify / fork the plugin to automatically do this for you.  
>
> https://github.com/GMOD/Apollo/blob/master/client/apollo/js/TrackConfigTransformer.js#L26
>
> Of course, I’m not sure whether or not that would be more work for you.
>
> Nathan
>
> On Jan 10, 2017, at 11:24 AM, Scott Cain <[hidden email]> wrote:
>
> Ah, who actually reads documentation, amiright? :-)  OK, now I only have to modify the store class of about 1300 tracks.
>
> On Tue, Jan 10, 2017 at 1:08 PM, Colin <[hidden email]> wrote:
>>
>> Hi Scott,
>> I think the problem you observe with projectionplugin is because the trackList needs some editing first.
>>
>> You have to need to edit the trackList.json to change the storeClass from JBrowse/Store/SeqFeature/Sequence to ProjectionPlugin/Store/SeqFeature/ReverseSequence, JBrowse/Store/SeqFeature/NCList to ProjectionPlugin/Store/SeqFeature/ReverseNCList, etc. The augmented storeClass implements the ability to do the reverse complement and can display non-reversed too.
>>
>>
>> -Colin
>>
>> On Tue, Jan 10, 2017 at 12:22 PM, Scott Cain <[hidden email]> wrote:
>>>
>>> Hi Nathan,
>>>
>>> Thanks for pointing that out, though it doesn't seem to work at the moment.  I installed it in WormBase's staging server:
>>>
>>> http://staging.wormbase.org/tools/genome/jbrowse-simple/full.html?data=data%2Fc_elegans_PRJNA13758&loc=MtDNA%3A9561..13794&tracks=Classical_alleles%2CPolymorphisms%2CCurated_Genes&highlight=
>>>
>>> It doesn't reverse complement the current view, but does have the exciting effect of taking you to a seemingly random location in the same sequence you're currently viewing.  It will help with people wanting to discover new things! :-)  I suspect the "random" place is a mirror image location, reflecting around the center of the sequence and is a result of a blown sign somewhere.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jan 10, 2017 at 11:48 AM, Nathan Dunn <[hidden email]> wrote:
>>>>
>>>>
>>>> Colin had written one for doing reverses explicitly in JBrowse:
>>>>
>>>> https://github.com/elsiklab/projectionplugin
>>>>
>>>> I’m sure it will need to be cleaned up a bit, but it had appeared to work when demoed.  
>>>>
>>>> The one we’re developing for Apollo will do more (combining arbitrary scaffolds in any orientation), but our initially foray will require an Apollo login and won’t be out for at least a month.  
>>>>
>>>> Nathan
>>>>
>>>> On Jan 10, 2017, at 7:35 AM, Scott Cain <[hidden email]> wrote:
>>>>
>>>> Hi Ian and Eric,
>>>>
>>>> We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:
>>>>
>>>> https://github.com/GMOD/jbrowse/issues/170
>>>>
>>>> Thanks,
>>>> Scott
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
>>>> Ontario Institute for Cancer Research
>>>> ------------------------------------------------------------------------------
>>>> Developer Access Program for Intel Xeon Phi Processors
>>>> Access to Intel Xeon Phi processor-based developer platforms.
>>>> With one year of Intel Parallel Studio XE.
>>>> Training and support from Colfax.
>>>> Order your platform today. http://sdm.link/xeonphi_______________________________________________
>>>> Gmod-ajax mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>> ------------------------------------------------------------------------------
>>> Developer Access Program for Intel Xeon Phi Processors
>>> Access to Intel Xeon Phi processor-based developer platforms.
>>> With one year of Intel Parallel Studio XE.
>>> Training and support from Colfax.
>>> Order your platform today. http://sdm.link/xeonphi
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
> Ontario Institute for Cancer Research
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax








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

------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
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Re: Flip orientation

nathandunn
In reply to this post by Suzanna Lewis-3

Suzi,

Our solution also integrates intra- and inter-genomic folding and the ability to build arbitrary scaffolds in various arbitrary orientations.  The ability to do reverse complement is one aspect of this, but we need to support ll of these. 

If folks are interested in determining how this might translate into a JBrowse only version, I would be happy to discuss it at PAG during the GMOD session. 

Nathan

On Jan 10, 2017, at 1:10 PM, Suzanna Lewis <[hidden email]> wrote:

Nathan, Ian and Eric

Forgive me, but isn't reverse-complement already working? (It's the same as "flip"). Is this a problem with core/essential/key fixes being made in Apollo, but not finding there way back into JBrowse.

It's very frustrating. I've been hammering on this for years now. I cannot emphasize enough how important this is. Will there ever be a day that dawns when it's done?

-S


On Tue, Jan 10, 2017 at 8:48 AM, Nathan Dunn <[hidden email]> wrote:

Colin had written one for doing reverses explicitly in JBrowse:


I’m sure it will need to be cleaned up a bit, but it had appeared to work when demoed.  

The one we’re developing for Apollo will do more (combining arbitrary scaffolds in any orientation), but our initially foray will require an Apollo login and won’t be out for at least a month.  

Nathan

On Jan 10, 2017, at 7:35 AM, Scott Cain <[hidden email]> wrote:

Hi Ian and Eric,

We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:


Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank" class="">216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi_______________________________________________
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With one year of Intel Parallel Studio XE.
Training and support from Colfax.
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Re: Flip orientation

Eric Yao
Nothing specific in JBrowse, except perhaps through 3rd party plugin.  (not graphical, far as I can see)
https://www.araport.org/jbrowse/user-guide

Apollo is the closest, I would say.

I don't plan to be at PAG, but if there's a way to be online at the GMOD discussions, that would be great.

On Tue, Jan 10, 2017 at 1:32 PM, Nathan Dunn <[hidden email]> wrote:

Suzi,

Our solution also integrates intra- and inter-genomic folding and the ability to build arbitrary scaffolds in various arbitrary orientations.  The ability to do reverse complement is one aspect of this, but we need to support ll of these. 

If folks are interested in determining how this might translate into a JBrowse only version, I would be happy to discuss it at PAG during the GMOD session. 

Nathan

On Jan 10, 2017, at 1:10 PM, Suzanna Lewis <[hidden email]> wrote:

Nathan, Ian and Eric

Forgive me, but isn't reverse-complement already working? (It's the same as "flip"). Is this a problem with core/essential/key fixes being made in Apollo, but not finding there way back into JBrowse.

It's very frustrating. I've been hammering on this for years now. I cannot emphasize enough how important this is. Will there ever be a day that dawns when it's done?

-S


On Tue, Jan 10, 2017 at 8:48 AM, Nathan Dunn <[hidden email]> wrote:

Colin had written one for doing reverses explicitly in JBrowse:


I’m sure it will need to be cleaned up a bit, but it had appeared to work when demoed.  

The one we’re developing for Apollo will do more (combining arbitrary scaffolds in any orientation), but our initially foray will require an Apollo login and won’t be out for at least a month.  

Nathan

On Jan 10, 2017, at 7:35 AM, Scott Cain <[hidden email]> wrote:

Hi Ian and Eric,

We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:


Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax


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With one year of Intel Parallel Studio XE.
Training and support from Colfax.
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Re: Flip orientation

Suzanna Lewis-3
Eric (and Ian)

My point is that, by definition, this means that JBrowse is BROKEN.

Being unable to support coordinate transforms is a big flaw.  This type of functionality must be in the core. Reverse complement at the very least. After all, it is supposed to be able to be useful to biologists, and without rev-comp it cannot accomplish this.

-S


On Wed, Jan 11, 2017 at 11:55 AM, Eric Yao <[hidden email]> wrote:
Nothing specific in JBrowse, except perhaps through 3rd party plugin.  (not graphical, far as I can see)
https://www.araport.org/jbrowse/user-guide

Apollo is the closest, I would say.

I don't plan to be at PAG, but if there's a way to be online at the GMOD discussions, that would be great.

On Tue, Jan 10, 2017 at 1:32 PM, Nathan Dunn <[hidden email]> wrote:

Suzi,

Our solution also integrates intra- and inter-genomic folding and the ability to build arbitrary scaffolds in various arbitrary orientations.  The ability to do reverse complement is one aspect of this, but we need to support ll of these. 

If folks are interested in determining how this might translate into a JBrowse only version, I would be happy to discuss it at PAG during the GMOD session. 

Nathan

On Jan 10, 2017, at 1:10 PM, Suzanna Lewis <[hidden email]> wrote:

Nathan, Ian and Eric

Forgive me, but isn't reverse-complement already working? (It's the same as "flip"). Is this a problem with core/essential/key fixes being made in Apollo, but not finding there way back into JBrowse.

It's very frustrating. I've been hammering on this for years now. I cannot emphasize enough how important this is. Will there ever be a day that dawns when it's done?

-S


On Tue, Jan 10, 2017 at 8:48 AM, Nathan Dunn <[hidden email]> wrote:

Colin had written one for doing reverses explicitly in JBrowse:


I’m sure it will need to be cleaned up a bit, but it had appeared to work when demoed.  

The one we’re developing for Apollo will do more (combining arbitrary scaffolds in any orientation), but our initially foray will require an Apollo login and won’t be out for at least a month.  

Nathan

On Jan 10, 2017, at 7:35 AM, Scott Cain <[hidden email]> wrote:

Hi Ian and Eric,

We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:


Thanks,
Scott


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Re: Flip orientation

nathandunn

Well, broken is a pretty strong word.  

JBrowse is highly optimized for delivering single-organism, single-scaffold solutions views of various customizable genome features.  I don’t think it currently has an equal. 

However, I think in the horizon we need to address two things: synteny and projection / coordinate transformation (folding, reverse complement, scaffold assembly)

The solution in my mind in both cases involves in the establishment of an additional layer that will allow projection of the store model layer into arbitrary coordinates so that we can view and the model layers are not necessarily identical.  I think there have been a few stabs at this and I know it is in the queue.   

I am putting together a fairly portable solution in Apollo where it can do this projection on the server / client layer, but I think we can do better with an additional from JBrowse, though I realize this is non-trivial.

I have had brief discussions about this with Ian and Eric, though we all have a ton on our plates in addition to this.   

I’m looking forward to having a more informed discussion with whomever happens at PAG during the GMOD session that can turn into something actionable.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory
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On Jan 11, 2017, at 3:21 PM, Suzanna Lewis <[hidden email]> wrote:

Eric (and Ian)

My point is that, by definition, this means that JBrowse is BROKEN.

Being unable to support coordinate transforms is a big flaw.  This type of functionality must be in the core. Reverse complement at the very least. After all, it is supposed to be able to be useful to biologists, and without rev-comp it cannot accomplish this.

-S


On Wed, Jan 11, 2017 at 11:55 AM, Eric Yao <[hidden email]> wrote:
Nothing specific in JBrowse, except perhaps through 3rd party plugin.  (not graphical, far as I can see)
https://www.araport.org/jbrowse/user-guide

Apollo is the closest, I would say.

I don't plan to be at PAG, but if there's a way to be online at the GMOD discussions, that would be great.

On Tue, Jan 10, 2017 at 1:32 PM, Nathan Dunn <[hidden email]> wrote:

Suzi,

Our solution also integrates intra- and inter-genomic folding and the ability to build arbitrary scaffolds in various arbitrary orientations.  The ability to do reverse complement is one aspect of this, but we need to support ll of these. 

If folks are interested in determining how this might translate into a JBrowse only version, I would be happy to discuss it at PAG during the GMOD session. 

Nathan

On Jan 10, 2017, at 1:10 PM, Suzanna Lewis <[hidden email]> wrote:

Nathan, Ian and Eric

Forgive me, but isn't reverse-complement already working? (It's the same as "flip"). Is this a problem with core/essential/key fixes being made in Apollo, but not finding there way back into JBrowse.

It's very frustrating. I've been hammering on this for years now. I cannot emphasize enough how important this is. Will there ever be a day that dawns when it's done?

-S


On Tue, Jan 10, 2017 at 8:48 AM, Nathan Dunn <[hidden email]> wrote:

Colin had written one for doing reverses explicitly in JBrowse:


I’m sure it will need to be cleaned up a bit, but it had appeared to work when demoed.  

The one we’re developing for Apollo will do more (combining arbitrary scaffolds in any orientation), but our initially foray will require an Apollo login and won’t be out for at least a month.  

Nathan

On Jan 10, 2017, at 7:35 AM, Scott Cain <[hidden email]> wrote:

Hi Ian and Eric,

We got another request at WormBase for orientation flipping in JBrowse.  I don't remember if that is going to make it into 2.0, but I really hope so.  There is a feature request in github, but it's pretty old, opened by Rob and doesn't look like it's been touched in a while:


Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank" class="">216-392-3087
Ontario Institute for Cancer Research
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