add track key attribute from CSV metadata file

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add track key attribute from CSV metadata file

Loraine Guéguen
Hi,

Remained unanswered on the jbrowse / gmod-ajax list, I try my luck with
the apollo list :

I have a JBrowse instance (1.12.1) with >500 tracks.
I use faceted trackSelector, and the metadata are stored in a CSV file
loaded with JSON attribute "trackMetadata".

Each track has a short name (defined in the CSV file) which is a
human-readable name. I would like that this short name is displayed as
track "title" when the track is displayed on the browser, that is to
say, I'd like that this short name is used as "key" for the track.

Is it possible ?
(naming the short-name CSV column as "key" is not working)

And the best would be, for a track, that the key defined in the CSV file
overrides the key defined in the trackList.json file.

Looking forward to reading your answers.
Thanks

Loraine

--
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: add track key attribute from CSV metadata file

Deepak Unni
Hi Loraine,

Currently JBrowse treats 'key' as the human readable name and 'label' as a track's unique name. Both of these are defined in the trackList.json (and tracks.conf) where all track related configurations reside.
While you can specify multiple columns in the trackMetadata.csv, which can be treated as facets in the faceted browser, its not possible to use a separate column replace a track's 'key' attribute. 
This is because when the track is displayed, JBrowse genome view looks at trackList.json and all it sees is 'key' and 'label'. At the time of displaying the track itself, it doesn't look at trackMetadata.csv for that extra bit of information.

Although, it could be possible to write a plugin that enables JBrowse to read trackMetadata.csv and do a lookup where it finds any desired column given a unique track 'label'.

Hope this helps.

Cheers,

Deepak


On Fri, Jan 19, 2018 at 9:46 AM, Loraine Guéguen <[hidden email]> wrote:
Hi,

Remained unanswered on the jbrowse / gmod-ajax list, I try my luck with the apollo list :

I have a JBrowse instance (1.12.1) with >500 tracks.
I use faceted trackSelector, and the metadata are stored in a CSV file loaded with JSON attribute "trackMetadata".

Each track has a short name (defined in the CSV file) which is a human-readable name. I would like that this short name is displayed as track "title" when the track is displayed on the browser, that is to say, I'd like that this short name is used as "key" for the track.

Is it possible ?
(naming the short-name CSV column as "key" is not working)

And the best would be, for a track, that the key defined in the CSV file overrides the key defined in the trackList.json file.

Looking forward to reading your answers.
Thanks

Loraine

--
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: <a href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: add track key attribute from CSV metadata file

Deepak Unni
Hi Loraine,

I poked around a bit with JBrowse and realized that the functionality is straightforward to implement.
I went ahead and created a JBrowse plugin called RenameTracks (https://github.com/deepakunni3/RenameTracks).

You can download the plugin and use it with your JBrowse instance.

I realized that this use-case ought to be common, and it has come up before in our lab.

Let me know if you run into any issues. Alternatively, you could also raise issues on the GitHub repository as well.


Cheers,

Deepak


On Fri, Jan 19, 2018 at 3:04 PM, Deepak Unni <[hidden email]> wrote:
Hi Loraine,

Currently JBrowse treats 'key' as the human readable name and 'label' as a track's unique name. Both of these are defined in the trackList.json (and tracks.conf) where all track related configurations reside.
While you can specify multiple columns in the trackMetadata.csv, which can be treated as facets in the faceted browser, its not possible to use a separate column replace a track's 'key' attribute. 
This is because when the track is displayed, JBrowse genome view looks at trackList.json and all it sees is 'key' and 'label'. At the time of displaying the track itself, it doesn't look at trackMetadata.csv for that extra bit of information.

Although, it could be possible to write a plugin that enables JBrowse to read trackMetadata.csv and do a lookup where it finds any desired column given a unique track 'label'.

Hope this helps.

Cheers,

Deepak


On Fri, Jan 19, 2018 at 9:46 AM, Loraine Guéguen <[hidden email]> wrote:
Hi,

Remained unanswered on the jbrowse / gmod-ajax list, I try my luck with the apollo list :

I have a JBrowse instance (1.12.1) with >500 tracks.
I use faceted trackSelector, and the metadata are stored in a CSV file loaded with JSON attribute "trackMetadata".

Each track has a short name (defined in the CSV file) which is a human-readable name. I would like that this short name is displayed as track "title" when the track is displayed on the browser, that is to say, I'd like that this short name is used as "key" for the track.

Is it possible ?
(naming the short-name CSV column as "key" is not working)

And the best would be, for a track, that the key defined in the CSV file overrides the key defined in the trackList.json file.

Looking forward to reading your answers.
Thanks

Loraine

--
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: <a href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: add track key attribute from CSV metadata file

Loraine Guéguen
Great!
Thanks a lot!

Le 20/01/2018 19:38, Deepak Unni a écrit :
Hi Loraine,

I poked around a bit with JBrowse and realized that the functionality is straightforward to implement.
I went ahead and created a JBrowse plugin called RenameTracks (https://github.com/deepakunni3/RenameTracks).

You can download the plugin and use it with your JBrowse instance.

I realized that this use-case ought to be common, and it has come up before in our lab.

Let me know if you run into any issues. Alternatively, you could also raise issues on the GitHub repository as well.


Cheers,

Deepak


On Fri, Jan 19, 2018 at 3:04 PM, Deepak Unni <[hidden email]> wrote:
Hi Loraine,

Currently JBrowse treats 'key' as the human readable name and 'label' as a track's unique name. Both of these are defined in the trackList.json (and tracks.conf) where all track related configurations reside.
While you can specify multiple columns in the trackMetadata.csv, which can be treated as facets in the faceted browser, its not possible to use a separate column replace a track's 'key' attribute. 
This is because when the track is displayed, JBrowse genome view looks at trackList.json and all it sees is 'key' and 'label'. At the time of displaying the track itself, it doesn't look at trackMetadata.csv for that extra bit of information.

Although, it could be possible to write a plugin that enables JBrowse to read trackMetadata.csv and do a lookup where it finds any desired column given a unique track 'label'.

Hope this helps.

Cheers,

Deepak


On Fri, Jan 19, 2018 at 9:46 AM, Loraine Guéguen <[hidden email]> wrote:
Hi,

Remained unanswered on the jbrowse / gmod-ajax list, I try my luck with the apollo list :

I have a JBrowse instance (1.12.1) with >500 tracks.
I use faceted trackSelector, and the metadata are stored in a CSV file loaded with JSON attribute "trackMetadata".

Each track has a short name (defined in the CSV file) which is a human-readable name. I would like that this short name is displayed as track "title" when the track is displayed on the browser, that is to say, I'd like that this short name is used as "key" for the track.

Is it possible ?
(naming the short-name CSV column as "key" is not working)

And the best would be, for a track, that the key defined in the CSV file overrides the key defined in the trackList.json file.

Looking forward to reading your answers.
Thanks

Loraine

--
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: <a moz-do-not-send="true" href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: add track key attribute from CSV metadata file

Deepak Unni
You are welcome :)

On Mon, Jan 22, 2018 at 2:35 AM, Loraine Guéguen <[hidden email]> wrote:
Great!
Thanks a lot!


Le 20/01/2018 19:38, Deepak Unni a écrit :
Hi Loraine,

I poked around a bit with JBrowse and realized that the functionality is straightforward to implement.
I went ahead and created a JBrowse plugin called RenameTracks (https://github.com/deepakunni3/RenameTracks).

You can download the plugin and use it with your JBrowse instance.

I realized that this use-case ought to be common, and it has come up before in our lab.

Let me know if you run into any issues. Alternatively, you could also raise issues on the GitHub repository as well.


Cheers,

Deepak


On Fri, Jan 19, 2018 at 3:04 PM, Deepak Unni <[hidden email]> wrote:
Hi Loraine,

Currently JBrowse treats 'key' as the human readable name and 'label' as a track's unique name. Both of these are defined in the trackList.json (and tracks.conf) where all track related configurations reside.
While you can specify multiple columns in the trackMetadata.csv, which can be treated as facets in the faceted browser, its not possible to use a separate column replace a track's 'key' attribute. 
This is because when the track is displayed, JBrowse genome view looks at trackList.json and all it sees is 'key' and 'label'. At the time of displaying the track itself, it doesn't look at trackMetadata.csv for that extra bit of information.

Although, it could be possible to write a plugin that enables JBrowse to read trackMetadata.csv and do a lookup where it finds any desired column given a unique track 'label'.

Hope this helps.

Cheers,

Deepak


On Fri, Jan 19, 2018 at 9:46 AM, Loraine Guéguen <[hidden email][hidden email]> wrote:
Hi,

Remained unanswered on the jbrowse / gmod-ajax list, I try my luck with the apollo list :

I have a JBrowse instance (1.12.1) with >500 tracks.
I use faceted trackSelector, and the metadata are stored in a CSV file loaded with JSON attribute "trackMetadata".

Each track has a short name (defined in the CSV file) which is a human-readable name. I would like that this short name is displayed as track "title" when the track is displayed on the browser, that is to say, I'd like that this short name is used as "key" for the track.

Is it possible ?
(naming the short-name CSV column as "key" is not working)

And the best would be, for a track, that the key defined in the CSV file overrides the key defined in the trackList.json file.

Looking forward to reading your answers.
Thanks

Loraine

--
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: <a href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 


-- 
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: <a href="tel:+33%202%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.