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unload track

nelsonwd
I need to remove some obsolete tracks. I found a posting about how to do this
but it is pretty old:

http://generic-model-organism-system-database.450254.n5.nabble.com/load-unload-a-track-only-td454589.html#a454591
http://generic-model-organism-system-database.450254.n5.nabble.com/load-unload-a-track-only-td454589.html#a454591
<http://generic-model-organism-system-database.450254.n5.nabble.com/load-unload-a-track-only-td454589.html#a454591>  

What are the current best practices for removing a track?

Thanks,
Bill




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Fwd: unload track

girlwithglasses
Is there a recommended method of removing obsolete tracks in GBrowse? If not, can we come up with one and put it into the GBrowse documentation? See the message below:

---------- Forwarded message ----------
From: Bill Nelson <[hidden email]>
Date: Wed, Dec 12, 2012 at 4:40 PM
Subject: Re: [Gmod-gbrowse] unload track
To: Amelia Ireland <[hidden email]>


Hi Amelia, 
I used:
delete t.*,n.*, f.* from typelist t, name n, feature f where t.tag = 'conf_mRNA:TAIR9' and t.id = f.typeid and f.id = n.id;

I was worried that the name table was used to normalize out the redundancy of the feature names but there are a lot of duplicates in name so I don't think there was a problem.  

It would be good to have a best practices for something like this though. 

I do have another question though, I'll post it tomorrow.

Thanks,
Bill 

On Wed, Dec 12, 2012 at 4:17 PM, Amelia Ireland <[hidden email]> wrote:
Hello,

Did you get a response to your question, and if not, do you still need help with it?


On Wed, Dec 5, 2012 at 11:58 AM, Bill Nelson <[hidden email]> wrote:
I need to remove some obsolete tracks. I found a posting about how to do this
but it is pretty old:

http://generic-model-organism-system-database.450254.n5.nabble.com/load-unload-a-track-only-td454589.html#a454591
http://generic-model-organism-system-database.450254.n5.nabble.com/load-unload-a-track-only-td454589.html#a454591
<http://generic-model-organism-system-database.450254.n5.nabble.com/load-unload-a-track-only-td454589.html#a454591>

What are the current best practices for removing a track?

Thanks,
Bill




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Re: Fwd: unload track

Scott Cain
Hi Amelia and Bill,

There is not a standard way to remove data because there are multiple
data backends.  Generally, the easiest thing to do is to drop the
database and reload it with the data you want and without the data you
don't (of course, that's not what I'd do with Chado, but that's
different).  Bio::DB::SeqFeature::Store does have a delete script
(bp_seqfeautre_delete.pl) but I don't know how much that is used in
practice.

Scott


On Thu, Dec 13, 2012 at 11:28 AM, Amelia Ireland
<[hidden email]> wrote:

> Is there a recommended method of removing obsolete tracks in GBrowse? If
> not, can we come up with one and put it into the GBrowse documentation? See
> the message below:
>
> ---------- Forwarded message ----------
> From: Bill Nelson <[hidden email]>
> Date: Wed, Dec 12, 2012 at 4:40 PM
> Subject: Re: [Gmod-gbrowse] unload track
> To: Amelia Ireland <[hidden email]>
>
>
> Hi Amelia,
> I used:
> delete t.*,n.*, f.* from typelist t, name n, feature f where t.tag =
> 'conf_mRNA:TAIR9' and t.id = f.typeid and f.id = n.id;
>
> I was worried that the name table was used to normalize out the redundancy
> of the feature names but there are a lot of duplicates in name so I don't
> think there was a problem.
>
> It would be good to have a best practices for something like this though.
>
> I do have another question though, I'll post it tomorrow.
>
> Thanks,
> Bill
>
> On Wed, Dec 12, 2012 at 4:17 PM, Amelia Ireland <[hidden email]>
> wrote:
>>
>> Hello,
>>
>> Did you get a response to your question, and if not, do you still need
>> help with it?
>>
>>
>> On Wed, Dec 5, 2012 at 11:58 AM, Bill Nelson <[hidden email]>
>> wrote:
>>>
>>> I need to remove some obsolete tracks. I found a posting about how to do
>>> this
>>> but it is pretty old:
>>>
>>>
>>> http://generic-model-organism-system-database.450254.n5.nabble.com/load-unload-a-track-only-td454589.html#a454591
>>>
>>> http://generic-model-organism-system-database.450254.n5.nabble.com/load-unload-a-track-only-td454589.html#a454591
>>>
>>> <http://generic-model-organism-system-database.450254.n5.nabble.com/load-unload-a-track-only-td454589.html#a454591>
>>>
>>> What are the current best practices for removing a track?
>>>
>>> Thanks,
>>> Bill
>>>
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>> http://generic-model-organism-system-database.450254.n5.nabble.com/unload-track-tp5710562.html
>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
>>> Remotely access PCs and mobile devices and provide instant support
>>> Improve your efficiency, and focus on delivering more value-add services
>>> Discover what IT Professionals Know. Rescue delivers
>>> http://p.sf.net/sfu/logmein_12329d2d
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>>
>>
>> --
>> Amelia Ireland
>> GMOD Community Support || http://gmod.org
>
>
>
>
>
> --
> Amelia Ireland
> GMOD Community Support || http://gmod.org
>
> ------------------------------------------------------------------------------
> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
> Remotely access PCs and mobile devices and provide instant support
> Improve your efficiency, and focus on delivering more value-add services
> Discover what IT Professionals Know. Rescue delivers
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> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



--
------------------------------------------------------------------------
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: Fwd: unload track

Nathan Weeks
In reply to this post by nelsonwd
For the SoyBase GBrowse, I use a separate SQLite database for each
Bio::DB::SeqFeature::Store track. This makes removing a track is as
easy as "rm track.db", making a backup of a track while testing a new
version is simply "mv track.db track.db.bak; bp_seqfeature_load.pl -c
-d track.db...", etc.

Using a separate database for each track also allows one to customize
the search methods on a per-track basis, which helps performance when
searching via the "Landmark or Region" box (e.g., for some tracks, a
"fulltext" search may be warranted, while other tracks may not need to
be searched at all).

--
Nathan Weeks
IT Specialist
USDA-ARS Corn Insects and Crop Genetics Research Unit
http://weeks.public.iastate.edu/


On Thu, Dec 13, 2012 at 1:31 PM,
<[hidden email]> wrote:

> ------------------------------
>
> Message: 4
> Date: Thu, 13 Dec 2012 12:41:05 -0500
> From: Scott Cain <[hidden email]>
> Subject: Re: [Gmod-gbrowse] Fwd: unload track
> To: Amelia Ireland <[hidden email]>
> Cc: "[hidden email]"
>         <[hidden email]>
> Message-ID:
>         <[hidden email]>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Amelia and Bill,
>
> There is not a standard way to remove data because there are multiple
> data backends.  Generally, the easiest thing to do is to drop the
> database and reload it with the data you want and without the data you
> don't (of course, that's not what I'd do with Chado, but that's
> different).  Bio::DB::SeqFeature::Store does have a delete script
> (bp_seqfeautre_delete.pl) but I don't know how much that is used in
> practice.
>
> Scott
>
>
> On Thu, Dec 13, 2012 at 11:28 AM, Amelia Ireland
> <[hidden email]> wrote:
>> Is there a recommended method of removing obsolete tracks in GBrowse? If
>> not, can we come up with one and put it into the GBrowse documentation? See
>> the message below:
>>
>> ---------- Forwarded message ----------
>> From: Bill Nelson <[hidden email]>
>> Date: Wed, Dec 12, 2012 at 4:40 PM
>> Subject: Re: [Gmod-gbrowse] unload track
>> To: Amelia Ireland <[hidden email]>
>>
>>
>> Hi Amelia,
>> I used:
>> delete t.*,n.*, f.* from typelist t, name n, feature f where t.tag =
>> 'conf_mRNA:TAIR9' and t.id = f.typeid and f.id = n.id;
>>
>> I was worried that the name table was used to normalize out the redundancy
>> of the feature names but there are a lot of duplicates in name so I don't
>> think there was a problem.
>>
>> It would be good to have a best practices for something like this though.
>>
>> I do have another question though, I'll post it tomorrow.
>>
>> Thanks,
>> Bill
>>
>> On Wed, Dec 12, 2012 at 4:17 PM, Amelia Ireland <[hidden email]>
>> wrote:
>>>
>>> Hello,
>>>
>>> Did you get a response to your question, and if not, do you still need
>>> help with it?
>>>
>>>
>>> On Wed, Dec 5, 2012 at 11:58 AM, Bill Nelson <[hidden email]>
>>> wrote:
>>>>
>>>> I need to remove some obsolete tracks. I found a posting about how to do
>>>> this
>>>> but it is pretty old:
>>>>
>>>>
>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/load-unload-a-track-only-td454589.html#a454591
>>>>
>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/load-unload-a-track-only-td454589.html#a454591
>>>>
>>>> <http://generic-model-organism-system-database.450254.n5.nabble.com/load-unload-a-track-only-td454589.html#a454591>
>>>>
>>>> What are the current best practices for removing a track?
>>>>
>>>> Thanks,
>>>> Bill
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> View this message in context:
>>>> http://generic-model-organism-system-database.450254.n5.nabble.com/unload-track-tp5710562.html
>>>> Sent from the gmod-gbrowse mailing list archive at Nabble.com.
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
>>>> Remotely access PCs and mobile devices and provide instant support
>>>> Improve your efficiency, and focus on delivering more value-add services
>>>> Discover what IT Professionals Know. Rescue delivers
>>>> http://p.sf.net/sfu/logmein_12329d2d
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>>
>>>
>>>
>>> --
>>> Amelia Ireland
>>> GMOD Community Support || http://gmod.org
>>
>>
>>
>>
>>
>> --
>> Amelia Ireland
>> GMOD Community Support || http://gmod.org
>>
>> ------------------------------------------------------------------------------
>> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
>> Remotely access PCs and mobile devices and provide instant support
>> Improve your efficiency, and focus on delivering more value-add services
>> Discover what IT Professionals Know. Rescue delivers
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>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 13 Dec 2012 14:13:56 -0500
> From: Haiming Wang <[hidden email]>
> Subject: [Gmod-gbrowse] subtracks with bigWigSet (overlap)
> To: Gbrowse Mailing List <[hidden email]>
> Cc: "John E. Brestelli" <[hidden email]>
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> I've four bigwig files and can display them fine either as four subtracks or superimposed (two screenshots are attached). However, I'd like to superimpose "Unique plus/minus" and "NU plus/minus" separately, therefore, I will have two subtracks - Unique and Non-unique. I searched the mailing list and found a similar discussions, but just could not make it work. Can someone point me out how to configure it? Here is my gbrowse conf and metadata.index.
>
> [BigWigP16:database]
> db_adaptor    = Bio::DB::BigWigSet
> db_args       = -dir /home/hwang/projects/bigwig/GiardiaDB/P16
>
> [BigWigUniqueIntervals]
> #feature  = summary
> feature  = RUM:GUS
> database = BigWigP16
> glyph    = wiggle_xyplot
> min_score = -10
> max_score = +10
> height = 80
> bicolor_pivot = zero
> pos_color = blue
> neg_color = red
> key       = Bigwig set meta -  P16
> #bump  = overlap
> #opacity = 0.5
> subtrack select  = Expt tag_value expt
> subtrack table   = :Unique Unique ;
>                   :NU NU;
> scale = both
>
>
> ########## metadata.index file ######
>
> [RUM_NU_plus.bw]
> display_name = "NU plus"
> method       = RUM
> source       = GUS
> expt         = NU
>
> [RUM_NU_minus.bw]
> display_name = "NU minus"
> method       = RUM
> source       = GUS
> expt         = NU
>
> [RUM_Unique_plus.bw]
> display_name = "Unique plus"
> method       = RUM
> source       = GUS
> expt         = Unique
>
> [RUM_Unique_minus.bw]
> display_name = "Unique minus"
> method       = RUM
> source       = GUS
> expt         = Unique
>
>
> Thanks,
> -Haiming
>
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: subtracks_bigwigset.tiff
> Type: image/tiff
> Size: 95326 bytes
> Desc: not available
> -------------- next part --------------
>
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: subtrack_superimposed.tiff
> Type: image/tiff
> Size: 59698 bytes
> Desc: not available
>
> ------------------------------
>
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> End of Gmod-gbrowse Digest, Vol 79, Issue 8
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