Group_on behaviour in BAM tracks

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Group_on behaviour in BAM tracks

Keiran Raine
Hi all,

I'm wondering if anyone else has been able to produce 'group_on' style behaviour in the BAM tracks.

I have BAM data where I want to group the reads that contribute to a particular event grouped together, something like:

Event 1
 ---------------------
  --------------------
----------------------
    ------------------

Event 2
--------------
----------------
----------
------------

I had thought to do this with subtracks but you need to define all permutations in order to use them.

So I attempted to use group_on as follows:

group_on = sub { my $f = shift;
    my ($xc) = $f->attributes('XC');
    return $xc;
  }

Unfortunately this does not seem to affect the outcome of the display.

Can anyone help?

Thanks,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703






-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
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download Logger. Secure your free ArcSight Logger TODAY!
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Re: Group_on behaviour in BAM tracks

Timothy Parnell
Hi Keiran,

I believe the 'group_on' value must be a valid seqfeature method that the features can be sorted upon, e.g. strand, type, display_name, etc.

Have you tried simply
group_on = attributes('XC')

Tim

From: Keiran Raine <[hidden email]<mailto:[hidden email]>>
Date: Tue, 30 Aug 2011 04:51:05 -0600
To: gbrowse List <[hidden email]<mailto:[hidden email]>>
Subject: [Gmod-gbrowse] Group_on behaviour in BAM tracks

Hi all,

I'm wondering if anyone else has been able to produce 'group_on' style behaviour in the BAM tracks.

I have BAM data where I want to group the reads that contribute to a particular event grouped together, something like:

Event 1
 ---------------------
  --------------------
----------------------
    ------------------

Event 2
--------------
----------------
----------
------------

I had thought to do this with subtracks but you need to define all permutations in order to use them.

So I attempted to use group_on as follows:

group_on = sub { my $f = shift;
    my ($xc) = $f->attributes('XC');
    return $xc;
  }

Unfortunately this does not seem to affect the outcome of the display.

Can anyone help?

Thanks,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703
[hidden email]<mailto:[hidden email]>






-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Special Offer -- Download ArcSight Logger for FREE!
Finally, a world-class log management solution at an even better
price-free! And you'll get a free "Love Thy Logs" t-shirt when you
download Logger. Secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsisghtdev2dev
_______________________________________________
Gmod-gbrowse mailing list
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Re: Group_on behaviour in BAM tracks

Lincoln Stein
In reply to this post by Keiran Raine
It ought to work the way you want it to. Have you put in warnings after you retrieve the XC tag to make sure that the tag is being retrieved properly by the Bio::SamTools library?

Lincoln

On Tue, Aug 30, 2011 at 6:51 AM, Keiran Raine <[hidden email]> wrote:
Hi all,

I'm wondering if anyone else has been able to produce 'group_on' style behaviour in the BAM tracks.

I have BAM data where I want to group the reads that contribute to a particular event grouped together, something like:

Event 1
 ---------------------
  --------------------
----------------------
    ------------------

Event 2
--------------
----------------
----------
------------

I had thought to do this with subtracks but you need to define all permutations in order to use them.

So I attempted to use group_on as follows:

group_on = sub { my $f = shift;
    my ($xc) = $f->attributes('XC');
    return $xc;
  }

Unfortunately this does not seem to affect the outcome of the display.

Can anyone help?

Thanks,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703






-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Special Offer -- Download ArcSight Logger for FREE!
Finally, a world-class log management solution at an even better
price-free! And you'll get a free "Love Thy Logs" t-shirt when you
download Logger. Secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsisghtdev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
Special Offer -- Download ArcSight Logger for FREE!
Finally, a world-class log management solution at an even better
price-free! And you'll get a free "Love Thy Logs" t-shirt when you
download Logger. Secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsisghtdev2dev
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Re: Group_on behaviour in BAM tracks

Keiran Raine
Hi Lincoln,

As pointed out by Tim we only have access to the Bio::SeqFeature::Lite object at this point so it does not look like we can do this at present (unless my version is too out of date, 2.17).

Regards,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703





On 30 Aug 2011, at 22:17, Lincoln Stein wrote:

It ought to work the way you want it to. Have you put in warnings after you retrieve the XC tag to make sure that the tag is being retrieved properly by the Bio::SamTools library?

Lincoln

On Tue, Aug 30, 2011 at 6:51 AM, Keiran Raine <[hidden email]> wrote:
Hi all,

I'm wondering if anyone else has been able to produce 'group_on' style behaviour in the BAM tracks.

I have BAM data where I want to group the reads that contribute to a particular event grouped together, something like:

Event 1
 ---------------------
  --------------------
----------------------
    ------------------

Event 2
--------------
----------------
----------
------------

I had thought to do this with subtracks but you need to define all permutations in order to use them.

So I attempted to use group_on as follows:

group_on = sub { my $f = shift;
    my ($xc) = $f->attributes('XC');
    return $xc;
  }

Unfortunately this does not seem to affect the outcome of the display.

Can anyone help?

Thanks,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703






-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Special Offer -- Download ArcSight Logger for FREE!
Finally, a world-class log management solution at an even better
price-free! And you'll get a free "Love Thy Logs" t-shirt when you
download Logger. Secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsisghtdev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Special Offer -- Download ArcSight Logger for FREE!
Finally, a world-class log management solution at an even better
price-free! And you'll get a free "Love Thy Logs" t-shirt when you
download Logger. Secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsisghtdev2dev
_______________________________________________
Gmod-gbrowse mailing list
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Re: Group_on behaviour in BAM tracks

Lincoln Stein
I'll test it out and see what can be done.

Lincoln

On Wed, Aug 31, 2011 at 6:04 AM, Keiran Raine <[hidden email]> wrote:
Hi Lincoln,

As pointed out by Tim we only have access to the Bio::SeqFeature::Lite object at this point so it does not look like we can do this at present (unless my version is too out of date, 2.17).

Regards,


Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703





On 30 Aug 2011, at 22:17, Lincoln Stein wrote:

It ought to work the way you want it to. Have you put in warnings after you retrieve the XC tag to make sure that the tag is being retrieved properly by the Bio::SamTools library?

Lincoln

On Tue, Aug 30, 2011 at 6:51 AM, Keiran Raine <[hidden email]> wrote:
Hi all,

I'm wondering if anyone else has been able to produce 'group_on' style behaviour in the BAM tracks.

I have BAM data where I want to group the reads that contribute to a particular event grouped together, something like:

Event 1
 ---------------------
  --------------------
----------------------
    ------------------

Event 2
--------------
----------------
----------
------------

I had thought to do this with subtracks but you need to define all permutations in order to use them.

So I attempted to use group_on as follows:

group_on = sub { my $f = shift;
    my ($xc) = $f->attributes('XC');
    return $xc;
  }

Unfortunately this does not seem to affect the outcome of the display.

Can anyone help?

Thanks,

Keiran Raine
Senior Computer Biologist
The Cancer Genome Project
Ext: 7703






-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Special Offer -- Download ArcSight Logger for FREE!
Finally, a world-class log management solution at an even better
price-free! And you'll get a free "Love Thy Logs" t-shirt when you
download Logger. Secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsisghtdev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>


-- 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.



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
Special Offer -- Download ArcSight Logger for FREE!
Finally, a world-class log management solution at an even better
price-free! And you'll get a free "Love Thy Logs" t-shirt when you
download Logger. Secure your free ArcSight Logger TODAY!
http://p.sf.net/sfu/arcsisghtdev2dev
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse