[Gmod-ajax] Export data from several tracks

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[Gmod-ajax] Export data from several tracks

FredBGA

Hello

 

I would like to be able to export data from several tracks.

 

I tried to use the combination track in order to create an union of two (or more) tracks.

Then the “Save track data” link is functional but all attributes (as well as source, type, score) are lost.

Of course this is a twisted way to try to achieve what I wanted J so it’s not really a surprise.

 

But it’s really close to what I need, so could you help me ?

 

At least point me which files I could try to copy and then modify in order to create a kind of "combine track to be exported function".

 

Thank you for your help and ideas.

 

---

Fred

 


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Re: Export data from several tracks

nathandunn

What types of tracks are you trying to export? 

Also, is there a reason you couldn’t use the original raw files and merge there, or download the output and merge that?

Its definitely functionality I would like to see as well (if I understand you correctly).   You could also build a custom REST track that would take two or more tracks and do the same, but that seems like a lot of work to do something fairly simple. 

Nathan

On Nov 25, 2016, at 7:46 AM, SAPET, Frederic <[hidden email]> wrote:

Hello
 
I would like to be able to export data from several tracks.
 
I tried to use the combination track in order to create an union of two (or more) tracks.
Then the “Save track data” link is functional but all attributes (as well as source, type, score) are lost.
Of course this is a twisted way to try to achieve what I wanted J so it’s not really a surprise.
 
But it’s really close to what I need, so could you help me ?
 
At least point me which files I could try to copy and then modify in order to create a kind of "combine track to be exported function".
 
Thank you for your help and ideas. 
 
---
Fred
 
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Re: Export data from several tracks

FredBGA

Hello Nathan,

 

Every kind of track should be exportable (at least at the level of displayed region).

 

There is no reason I can’t use the original raw files because I’m the admin of the tool. But I meant for a “basic” user.

When they do data mining on a region, they often want to extract data (SNP data from several tracks, a coverage track etc…) in order to continue their work with other tools.

 

Of course I don't need (and don't want my users to) to export data from a whole chromosome or the entire genome. A limit could applied.

 

does it make more sense ?

 

Fred

 

De : Nathan Dunn [mailto:[hidden email]]
Envoyé : dimanche 27 novembre 2016 03:07
À : SAPET, Frederic <[hidden email]>
Cc : [hidden email]
Objet : Re: [Gmod-ajax] Export data from several tracks

 

 

What types of tracks are you trying to export? 

 

Also, is there a reason you couldn’t use the original raw files and merge there, or download the output and merge that?

 

Its definitely functionality I would like to see as well (if I understand you correctly).   You could also build a custom REST track that would take two or more tracks and do the same, but that seems like a lot of work to do something fairly simple. 

 

Nathan

 

On Nov 25, 2016, at 7:46 AM, SAPET, Frederic <[hidden email]> wrote:

 

Hello

 

I would like to be able to export data from several tracks.

 

I tried to use the combination track in order to create an union of two (or more) tracks.

Then the “Save track data” link is functional but all attributes (as well as source, type, score) are lost.

Of course this is a twisted way to try to achieve what I wanted J so it’s not really a surprise.

 

But it’s really close to what I need, so could you help me ?

 

At least point me which files I could try to copy and then modify in order to create a kind of "combine track to be exported function".

 

Thank you for your help and ideas. 

 

---

Fred

 

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Re: Export data from several tracks

nathandunn

Fred,

That makes sense.    You can definitely create a combo track (File/Track -> Add Combination Tracks) from SNP and HTML Feature track data and export that as you would any other data types, though I’m not sure that the filtering options (below) would be ideal.  In theory you can do the same for BAM tracks, but I haven’t gotten it to work in the examples I have. 

   


Nathan



On Nov 28, 2016, at 12:12 AM, SAPET, Frederic <[hidden email]> wrote:

Hello Nathan,
 
Every kind of track should be exportable (at least at the level of displayed region).
 
There is no reason I can’t use the original raw files because I’m the admin of the tool. But I meant for a “basic” user.
When they do data mining on a region, they often want to extract data (SNP data from several tracks, a coverage track etc…) in order to continue their work with other tools.
 
Of course I don't need (and don't want my users to) to export data from a whole chromosome or the entire genome. A limit could applied.
 
does it make more sense ?
 
Fred
 
De : Nathan Dunn [[hidden email]] 
Envoyé : dimanche 27 novembre 2016 03:07
À : SAPET, Frederic <[hidden email]>
Cc : [hidden email]
Objet : Re: [Gmod-ajax] Export data from several tracks
 
 
What types of tracks are you trying to export? 
 
Also, is there a reason you couldn’t use the original raw files and merge there, or download the output and merge that?
 
Its definitely functionality I would like to see as well (if I understand you correctly).   You could also build a custom REST track that would take two or more tracks and do the same, but that seems like a lot of work to do something fairly simple. 
 
Nathan
 
On Nov 25, 2016, at 7:46 AM, SAPET, Frederic <[hidden email]> wrote:
 
Hello
 
I would like to be able to export data from several tracks.
 
I tried to use the combination track in order to create an union of two (or more) tracks.
Then the “Save track data” link is functional but all attributes (as well as source, type, score) are lost.
Of course this is a twisted way to try to achieve what I wanted J so it’s not really a surprise.
 
But it’s really close to what I need, so could you help me ?
 
At least point me which files I could try to copy and then modify in order to create a kind of "combine track to be exported function".
 
Thank you for your help and ideas. 
 
---
Fred
 
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Re: Export data from several tracks

FredBGA

Hi,

 

I will need to add a new  option “keep tags”.

 

This export of my first track is :

 

##gff-version 3

##sequence-region Chr1 1 5479784

Chr1      SNP1     snp        112045  112045  .              +             .              alleles=A/T;Name=SNP4835;quality=Low;ID=4835

 

The second track :

##gff-version 3

##sequence-region Chr1 1 5479784

Chr1      SNP2     snp        112103  112103  .              -              .              alleles=T/C;Name=SNP-89524575;quality=Low;genetic_position=NA;ID=8952457;Alias=crt028004

 

The export of the combination track (union of the two above tracks) is :

##gff-version 3

##sequence-region Chr1 1 5479784

Chr1      .              .              112045  112045  .              +             .              .

Chr1      .              .              112103  112103  .              -              .              .

###

 

I would like to have :

##gff-version 3

##sequence-region Chr1 1 5479784

Chr1      SNP1     snp        112045  112045  .              +             .              alleles=A/T;Name=SNP4835;quality=Low;ID=4835

Chr1      SNP2     snp        112103  112103  .              -              .              alleles=T/C;Name=SNP-89524575;quality=Low;genetic_position=NA;ID=8952457;Alias=crt028004

 

So it’s really close to what I need !

 

Fred

 

De : Nathan Dunn [mailto:[hidden email]]
Envoyé : lundi 28 novembre 2016 18:07
À : SAPET, Frederic <[hidden email]>
Cc : [hidden email]
Objet : Re: [Gmod-ajax] Export data from several tracks

 

 

Fred,

 

That makes sense.    You can definitely create a combo track (File/Track -> Add Combination Tracks) from SNP and HTML Feature track data and export that as you would any other data types, though I’m not sure that the filtering options (below) would be ideal.  In theory you can do the same for BAM tracks, but I haven’t gotten it to work in the examples I have. 

 

cid:68569F11-4863-4C44-8B29-1107A00B769C   

 

 

Nathan

 

 

 

On Nov 28, 2016, at 12:12 AM, SAPET, Frederic <[hidden email]> wrote:

 

Hello Nathan,

 

Every kind of track should be exportable (at least at the level of displayed region).

 

There is no reason I can’t use the original raw files because I’m the admin of the tool. But I meant for a “basic” user.

When they do data mining on a region, they often want to extract data (SNP data from several tracks, a coverage track etc…) in order to continue their work with other tools.

 

Of course I don't need (and don't want my users to) to export data from a whole chromosome or the entire genome. A limit could applied.

 

does it make more sense ?

 

Fred

 

De : Nathan Dunn [[hidden email]] 
Envoyé : dimanche 27 novembre 2016 03:07
À : SAPET, Frederic <
[hidden email]>
Cc : 
[hidden email]
Objet : Re: [Gmod-ajax] Export data from several tracks

 

 

What types of tracks are you trying to export? 

 

Also, is there a reason you couldn’t use the original raw files and merge there, or download the output and merge that?

 

Its definitely functionality I would like to see as well (if I understand you correctly).   You could also build a custom REST track that would take two or more tracks and do the same, but that seems like a lot of work to do something fairly simple. 

 

Nathan

 

On Nov 25, 2016, at 7:46 AM, SAPET, Frederic <[hidden email]> wrote:

 

Hello

 

I would like to be able to export data from several tracks.

 

I tried to use the combination track in order to create an union of two (or more) tracks.

Then the “Save track data” link is functional but all attributes (as well as source, type, score) are lost.

Of course this is a twisted way to try to achieve what I wanted J so it’s not really a surprise.

 

But it’s really close to what I need, so could you help me ?

 

At least point me which files I could try to copy and then modify in order to create a kind of "combine track to be exported function".

 

Thank you for your help and ideas. 

 

---

Fred

 

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