Adding new locations for existing features in Chado

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

Adding new locations for existing features in Chado

Surya Saha
Hi Everybody,

I am CCing the gbrowse list since its relevant for folks there using Chado.

I am using the gmod_bulk_load_gff3.pl script from the Chado SVN checkout. A new row is created in the feature table when I upload a GFF record containing the new location for a gene on a new reference chromosome. The uniquename for the new row is the name appended by the new feature_id. A row is also created in featureloc for the new feature_id.

Is there a reason why simply a new row is not created in featureloc with the new coordinates and the old gene feature_id? How are people dealing with cases where new coordinates (from new reference assembly) have to be added for a gene already in the database? Thanks

-Surya


--

Surya Saha
Department of Plant Pathology, 
Cornell University, NY, USA.
Sol Genomics Network, 
Boyce Thompson Institute, Ithaca, NY, USA.

------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: Adding new locations for existing features in Chado

Siddhartha Basu
Hi Surya,
The bulk loader as far as the doc says does not support upsert(update if
present) of an existing feature. From the pod ...

--------------
Deletes and updates via GFF
    There is rudimentary support for modifying the features in an
    existing database via GFF.  Currently, there is only support
    for deleting.  In order to delete, the GFF
    line must have a custom tag in the ninth column,
   'CRUD' (for Create, Replace, Update and Delete)
    and have a recognized value.  Currently the two
    recognized values are
    CRUD=delete and CRUD=delete-all.

However, you might use delete and fresh insert keeping in mind the
consequences involved(explained in the doc).
The other alternate would be the write a custom update script to parse GFF3 check for
the presence of feature and update one by one as neccessary. If you want bulk style,
one approach would be to upload the GFF3 to a temp table and then make a bulk update
statment between temp and your chado table. This is more or less the
approach i am using generally.

thanks,
-sidd





On Mon, 06 Jan 2014, Surya Saha wrote:

>    Hi Everybody,
>    I am CCing the gbrowse list since its relevant for folks there using
>    Chado.
>    I am using the gmod_bulk_load_gff3.pl script from the Chado SVN checkout.
>    A new row is created in the feature table when I upload a GFF record
>    containing the new location for a gene on a new reference chromosome. The
>    uniquename for the new row is the name appended by the new feature_id. A
>    row is also created in featureloc for the new feature_id.
>    Is there a reason why simply a new row is not created in featureloc with
>    the new coordinates and the old gene feature_id? How are people dealing
>    with cases where new coordinates (from new reference assembly) have to be
>    added for a gene already in the database? Thanks
>    -Surya
>    --
>    Surya Saha
>    Department of Plant Pathology,
>    Cornell University, NY, USA.
>    Sol Genomics Network,
>    Boyce Thompson Institute, Ithaca, NY, USA.
>    http://www.linkedin.com/in/suryasaha
>    Twitter: https://twitter.com/SahaSurya

> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk

> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: Adding new locations for existing features in Chado

Surya Saha
Hi Siddartha,

Thanks for the input. The current loader also uses the intermediate temp file method. Do you have your code on github? I might end up writing a new loader that checks for existing feature's and handles them appropriately. Its surprising that this common use case is not addressed in the current loader. 

@Scott: Did you have any thoughts on this?

-Surya
 


On Tue, Jan 7, 2014 at 11:39 AM, Siddhartha Basu <[hidden email]> wrote:
Hi Surya,
The bulk loader as far as the doc says does not support upsert(update if
present) of an existing feature. From the pod ...

--------------
Deletes and updates via GFF
    There is rudimentary support for modifying the features in an
    existing database via GFF.  Currently, there is only support
    for deleting.  In order to delete, the GFF
    line must have a custom tag in the ninth column,
   'CRUD' (for Create, Replace, Update and Delete)
    and have a recognized value.  Currently the two
    recognized values are
    CRUD=delete and CRUD=delete-all.

However, you might use delete and fresh insert keeping in mind the
consequences involved(explained in the doc).
The other alternate would be the write a custom update script to parse GFF3 check for
the presence of feature and update one by one as neccessary. If you want bulk style,
one approach would be to upload the GFF3 to a temp table and then make a bulk update
statment between temp and your chado table. This is more or less the
approach i am using generally.

thanks,
-sidd





On Mon, 06 Jan 2014, Surya Saha wrote:

>    Hi Everybody,
>    I am CCing the gbrowse list since its relevant for folks there using
>    Chado.
>    I am using the gmod_bulk_load_gff3.pl script from the Chado SVN checkout.
>    A new row is created in the feature table when I upload a GFF record
>    containing the new location for a gene on a new reference chromosome. The
>    uniquename for the new row is the name appended by the new feature_id. A
>    row is also created in featureloc for the new feature_id.
>    Is there a reason why simply a new row is not created in featureloc with
>    the new coordinates and the old gene feature_id? How are people dealing
>    with cases where new coordinates (from new reference assembly) have to be
>    added for a gene already in the database? Thanks
>    -Surya
>    --
>    Surya Saha
>    Department of Plant Pathology,
>    Cornell University, NY, USA.
>    Sol Genomics Network,
>    Boyce Thompson Institute, Ithaca, NY, USA.
>    http://www.linkedin.com/in/suryasaha
>    Twitter: https://twitter.com/SahaSurya

> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk

> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema



--

Surya Saha
Department of Plant Pathology, 
Cornell University, NY, USA.
Sol Genomics Network, 
Boyce Thompson Institute, Ithaca, NY, USA.

------------------------------------------------------------------------------
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: Adding new locations for existing features in Chado

Siddhartha Basu
Hi Surya,
Here is a quick code showing the idea of the bulk update..
https://gist.github.com/cybersiddhu/8378221
I haven't run it though, but should give you an idea to start it.
Here is another write up about the way i am structuring my bulk upload
programs ...
http://dictybase.github.io/blog/2013/09/18/chado-loader-design/
And this is a gff3-loader that i haved written more or less following
the above principles, still work in progress though, and of course it
is not going to upsert, but the reasoning for this is different.
https://github.com/dictyBase/Modware-Loader/blob/develop/lib/Modware/Load/Command/gff3tochado.pm

Hope this helps.
Let me know if you have any questions.
thanks,
-siddhartha



On Tue, 07 Jan 2014, Surya Saha wrote:

>    Hi Siddartha,
>    Thanks for the input. The current loader also uses the intermediate temp
>    file method. Do you have your code on github? I might end up writing a new
>    loader that checks for existing feature's and handles them appropriately.
>    Its surprising that this common use case is not addressed in the current
>    loader.
>    @Scott: Did you have any thoughts on this?
>    -Surya
>    
>
>    On Tue, Jan 7, 2014 at 11:39 AM, Siddhartha Basu <[hidden email]>
>    wrote:
>
>      Hi Surya,
>      The bulk loader as far as the doc says does not support upsert(update if
>      present) of an existing feature. From the pod ...
>
>      --------------
>      Deletes and updates via GFF
>          There is rudimentary support for modifying the features in an
>          existing database via GFF.  Currently, there is only support
>          for deleting.  In order to delete, the GFF
>          line must have a custom tag in the ninth column,
>         'CRUD' (for Create, Replace, Update and Delete)
>          and have a recognized value.  Currently the two
>          recognized values are
>          CRUD=delete and CRUD=delete-all.
>
>      However, you might use delete and fresh insert keeping in mind the
>      consequences involved(explained in the doc).
>      The other alternate would be the write a custom update script to parse
>      GFF3 check for
>      the presence of feature and update one by one as neccessary. If you want
>      bulk style,
>      one approach would be to upload the GFF3 to a temp table and then make a
>      bulk update
>      statment between temp and your chado table. This is more or less the
>      approach i am using generally.
>
>      thanks,
>      -sidd
>
>      On Mon, 06 Jan 2014, Surya Saha wrote:
>
>      >    Hi Everybody,
>      >    I am CCing the gbrowse list since its relevant for folks there
>      using
>      >    Chado.
>      >    I am using the gmod_bulk_load_gff3.pl script from the Chado SVN
>      checkout.
>      >    A new row is created in the feature table when I upload a GFF
>      record
>      >    containing the new location for a gene on a new reference
>      chromosome. The
>      >    uniquename for the new row is the name appended by the new
>      feature_id. A
>      >    row is also created in featureloc for the new feature_id.
>      >    Is there a reason why simply a new row is not created in featureloc
>      with
>      >    the new coordinates and the old gene feature_id? How are people
>      dealing
>      >    with cases where new coordinates (from new reference assembly) have
>      to be
>      >    added for a gene already in the database? Thanks
>      >    -Surya
>      >    --
>      >    Surya Saha
>      >    Department of Plant Pathology,
>      >    Cornell University, NY, USA.
>      >    Sol Genomics Network,
>      >    Boyce Thompson Institute, Ithaca, NY, USA.
>      >    http://www.linkedin.com/in/suryasaha
>      >    Twitter: https://twitter.com/SahaSurya
>
>      >
>      ------------------------------------------------------------------------------
>      > Rapidly troubleshoot problems before they affect your business. Most
>      IT
>      > organizations don't have a clear picture of how application
>      performance
>      > affects their revenue. With AppDynamics, you get 100% visibility into
>      your
>      > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of
>      AppDynamics Pro!
>      >
>      http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>
>      > _______________________________________________
>      > Gmod-schema mailing list
>      > [hidden email]
>      > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>      ------------------------------------------------------------------------------
>      Rapidly troubleshoot problems before they affect your business. Most IT
>      organizations don't have a clear picture of how application performance
>      affects their revenue. With AppDynamics, you get 100% visibility into
>      your
>      Java,.NET, & PHP application. Start your 15-day FREE TRIAL of
>      AppDynamics Pro!
>      http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>      _______________________________________________
>      Gmod-schema mailing list
>      [hidden email]
>      https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>    --
>    Surya Saha
>    Department of Plant Pathology,
>    Cornell University, NY, USA.
>    Sol Genomics Network,
>    Boyce Thompson Institute, Ithaca, NY, USA.
>    http://www.linkedin.com/in/suryasaha
>    Twitter: https://twitter.com/SahaSurya

> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk

> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: Adding new locations for existing features in Chado

Surya Saha
Hi Siddartha,

Very helpful indeed. Thank you for the detailed reply. We are both on the same page re the bulk loader with DBIx::Class and having a staging area on disk. I have not explored SQL::Library but it looks interesting. There is a skeleton in place at https://github.com/solgenomics/bio-chado-loader that I will be adding to.

I will be in touch. Thanks again.

Best,
Surya








On Sat, Jan 11, 2014 at 6:22 PM, Siddhartha Basu <[hidden email]> wrote:
Hi Surya,
Here is a quick code showing the idea of the bulk update..
https://gist.github.com/cybersiddhu/8378221
I haven't run it though, but should give you an idea to start it.
Here is another write up about the way i am structuring my bulk upload
programs ...
http://dictybase.github.io/blog/2013/09/18/chado-loader-design/
And this is a gff3-loader that i haved written more or less following
the above principles, still work in progress though, and of course it
is not going to upsert, but the reasoning for this is different.
https://github.com/dictyBase/Modware-Loader/blob/develop/lib/Modware/Load/Command/gff3tochado.pm

Hope this helps.
Let me know if you have any questions.
thanks,
-siddhartha



On Tue, 07 Jan 2014, Surya Saha wrote:

>    Hi Siddartha,
>    Thanks for the input. The current loader also uses the intermediate temp
>    file method. Do you have your code on github? I might end up writing a new
>    loader that checks for existing feature's and handles them appropriately.
>    Its surprising that this common use case is not addressed in the current
>    loader.
>    @Scott: Did you have any thoughts on this?
>    -Surya
>
>
>    On Tue, Jan 7, 2014 at 11:39 AM, Siddhartha Basu <[hidden email]>
>    wrote:
>
>      Hi Surya,
>      The bulk loader as far as the doc says does not support upsert(update if
>      present) of an existing feature. From the pod ...
>
>      --------------
>      Deletes and updates via GFF
>          There is rudimentary support for modifying the features in an
>          existing database via GFF.  Currently, there is only support
>          for deleting.  In order to delete, the GFF
>          line must have a custom tag in the ninth column,
>         'CRUD' (for Create, Replace, Update and Delete)
>          and have a recognized value.  Currently the two
>          recognized values are
>          CRUD=delete and CRUD=delete-all.
>
>      However, you might use delete and fresh insert keeping in mind the
>      consequences involved(explained in the doc).
>      The other alternate would be the write a custom update script to parse
>      GFF3 check for
>      the presence of feature and update one by one as neccessary. If you want
>      bulk style,
>      one approach would be to upload the GFF3 to a temp table and then make a
>      bulk update
>      statment between temp and your chado table. This is more or less the
>      approach i am using generally.
>
>      thanks,
>      -sidd
>
>      On Mon, 06 Jan 2014, Surya Saha wrote:
>
>      >    Hi Everybody,
>      >    I am CCing the gbrowse list since its relevant for folks there
>      using
>      >    Chado.
>      >    I am using the gmod_bulk_load_gff3.pl script from the Chado SVN
>      checkout.
>      >    A new row is created in the feature table when I upload a GFF
>      record
>      >    containing the new location for a gene on a new reference
>      chromosome. The
>      >    uniquename for the new row is the name appended by the new
>      feature_id. A
>      >    row is also created in featureloc for the new feature_id.
>      >    Is there a reason why simply a new row is not created in featureloc
>      with
>      >    the new coordinates and the old gene feature_id? How are people
>      dealing
>      >    with cases where new coordinates (from new reference assembly) have
>      to be
>      >    added for a gene already in the database? Thanks
>      >    -Surya
>      >    --
>      >    Surya Saha
>      >    Department of Plant Pathology,
>      >    Cornell University, NY, USA.
>      >    Sol Genomics Network,
>      >    Boyce Thompson Institute, Ithaca, NY, USA.
>      >    http://www.linkedin.com/in/suryasaha
>      >    Twitter: https://twitter.com/SahaSurya
>
>      >
>      ------------------------------------------------------------------------------
>      > Rapidly troubleshoot problems before they affect your business. Most
>      IT
>      > organizations don't have a clear picture of how application
>      performance
>      > affects their revenue. With AppDynamics, you get 100% visibility into
>      your
>      > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of
>      AppDynamics Pro!
>      >
>      http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>
>      > _______________________________________________
>      > Gmod-schema mailing list
>      > [hidden email]
>      > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>      ------------------------------------------------------------------------------
>      Rapidly troubleshoot problems before they affect your business. Most IT
>      organizations don't have a clear picture of how application performance
>      affects their revenue. With AppDynamics, you get 100% visibility into
>      your
>      Java,.NET, & PHP application. Start your 15-day FREE TRIAL of
>      AppDynamics Pro!
>      http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>      _______________________________________________
>      Gmod-schema mailing list
>      [hidden email]
>      https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>    --
>    Surya Saha
>    Department of Plant Pathology,
>    Cornell University, NY, USA.
>    Sol Genomics Network,
>    Boyce Thompson Institute, Ithaca, NY, USA.
>    http://www.linkedin.com/in/suryasaha
>    Twitter: https://twitter.com/SahaSurya

> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk

> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema



--

Surya Saha
Department of Plant Pathology, 
Cornell University, NY, USA.
Sol Genomics Network, 
Boyce Thompson Institute, Ithaca, NY, USA.

------------------------------------------------------------------------------
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: Adding new locations for existing features in Chado

Siddhartha Basu
Hi Surya,
Glad to help.
bio-chado-loader seems to be a nice module, would be easy to integrate
in our workflow if require. I might need the orthomcl loader at some
point.

thanks,
-sidd

On Sun, 12 Jan 2014, Surya Saha wrote:

>    Hi Siddartha,
>    Very helpful indeed. Thank you for the detailed reply. We are both on the
>    same page re the bulk loader with DBIx::Class and having a staging area on
>    disk. I have not explored SQL::Library but it looks interesting. There is
>    a skeleton in place at https://github.com/solgenomics/bio-chado-loader
>    that I will be adding to.
>    I will be in touch. Thanks again.
>    Best,
>    Surya
>
>    On Sat, Jan 11, 2014 at 6:22 PM, Siddhartha Basu <[hidden email]>
>    wrote:
>
>      Hi Surya,
>      Here is a quick code showing the idea of the bulk update..
>      https://gist.github.com/cybersiddhu/8378221
>      I haven't run it though, but should give you an idea to start it.
>      Here is another write up about the way i am structuring my bulk upload
>      programs ...
>      http://dictybase.github.io/blog/2013/09/18/chado-loader-design/
>      And this is a gff3-loader that i haved written more or less following
>      the above principles, still work in progress though, and of course it
>      is not going to upsert, but the reasoning for this is different.
>      https://github.com/dictyBase/Modware-Loader/blob/develop/lib/Modware/Load/Command/gff3tochado.pm
>
>      Hope this helps.
>      Let me know if you have any questions.
>      thanks,
>      -siddhartha
>
>      On Tue, 07 Jan 2014, Surya Saha wrote:
>
>      >    Hi Siddartha,
>      >    Thanks for the input. The current loader also uses the intermediate
>      temp
>      >    file method. Do you have your code on github? I might end up
>      writing a new
>      >    loader that checks for existing feature's and handles them
>      appropriately.
>      >    Its surprising that this common use case is not addressed in the
>      current
>      >    loader.
>      >    @Scott: Did you have any thoughts on this?
>      >    -Surya
>      >
>      >
>      >    On Tue, Jan 7, 2014 at 11:39 AM, Siddhartha Basu
>      <[hidden email]>
>      >    wrote:
>      >
>      >      Hi Surya,
>      >      The bulk loader as far as the doc says does not support
>      upsert(update if
>      >      present) of an existing feature. From the pod ...
>      >
>      >      --------------
>      >      Deletes and updates via GFF
>      >          There is rudimentary support for modifying the features in an
>      >          existing database via GFF.  Currently, there is only support
>      >          for deleting.  In order to delete, the GFF
>      >          line must have a custom tag in the ninth column,
>      >         'CRUD' (for Create, Replace, Update and Delete)
>      >          and have a recognized value.  Currently the two
>      >          recognized values are
>      >          CRUD=delete and CRUD=delete-all.
>      >
>      >      However, you might use delete and fresh insert keeping in mind
>      the
>      >      consequences involved(explained in the doc).
>      >      The other alternate would be the write a custom update script to
>      parse
>      >      GFF3 check for
>      >      the presence of feature and update one by one as neccessary. If
>      you want
>      >      bulk style,
>      >      one approach would be to upload the GFF3 to a temp table and then
>      make a
>      >      bulk update
>      >      statment between temp and your chado table. This is more or less
>      the
>      >      approach i am using generally.
>      >
>      >      thanks,
>      >      -sidd
>      >
>      >      On Mon, 06 Jan 2014, Surya Saha wrote:
>      >
>      >      >    Hi Everybody,
>      >      >    I am CCing the gbrowse list since its relevant for folks
>      there
>      >      using
>      >      >    Chado.
>      >      >    I am using the gmod_bulk_load_gff3.pl script from the Chado
>      SVN
>      >      checkout.
>      >      >    A new row is created in the feature table when I upload a
>      GFF
>      >      record
>      >      >    containing the new location for a gene on a new reference
>      >      chromosome. The
>      >      >    uniquename for the new row is the name appended by the new
>      >      feature_id. A
>      >      >    row is also created in featureloc for the new feature_id.
>      >      >    Is there a reason why simply a new row is not created in
>      featureloc
>      >      with
>      >      >    the new coordinates and the old gene feature_id? How are
>      people
>      >      dealing
>      >      >    with cases where new coordinates (from new reference
>      assembly) have
>      >      to be
>      >      >    added for a gene already in the database? Thanks
>      >      >    -Surya
>      >      >    --
>      >      >    Surya Saha
>      >      >    Department of Plant Pathology,
>      >      >    Cornell University, NY, USA.
>      >      >    Sol Genomics Network,
>      >      >    Boyce Thompson Institute, Ithaca, NY, USA.
>      >      >    http://www.linkedin.com/in/suryasaha
>      >      >    Twitter: https://twitter.com/SahaSurya
>      >
>      >      >
>      >    
>       ------------------------------------------------------------------------------
>      >      > Rapidly troubleshoot problems before they affect your business.
>      Most
>      >      IT
>      >      > organizations don't have a clear picture of how application
>      >      performance
>      >      > affects their revenue. With AppDynamics, you get 100%
>      visibility into
>      >      your
>      >      > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of
>      >      AppDynamics Pro!
>      >      >
>      >    
>       http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>      >
>      >      > _______________________________________________
>      >      > Gmod-schema mailing list
>      >      > [hidden email]
>      >      > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>      >
>      >    
>       ------------------------------------------------------------------------------
>      >      Rapidly troubleshoot problems before they affect your business.
>      Most IT
>      >      organizations don't have a clear picture of how application
>      performance
>      >      affects their revenue. With AppDynamics, you get 100% visibility
>      into
>      >      your
>      >      Java,.NET, & PHP application. Start your 15-day FREE TRIAL of
>      >      AppDynamics Pro!
>      >    
>       http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>      >      _______________________________________________
>      >      Gmod-schema mailing list
>      >      [hidden email]
>      >      https://lists.sourceforge.net/lists/listinfo/gmod-schema
>      >
>      >    --
>      >    Surya Saha
>      >    Department of Plant Pathology,
>      >    Cornell University, NY, USA.
>      >    Sol Genomics Network,
>      >    Boyce Thompson Institute, Ithaca, NY, USA.
>      >    http://www.linkedin.com/in/suryasaha
>      >    Twitter: https://twitter.com/SahaSurya
>
>      >
>      ------------------------------------------------------------------------------
>      > Rapidly troubleshoot problems before they affect your business. Most
>      IT
>      > organizations don't have a clear picture of how application
>      performance
>      > affects their revenue. With AppDynamics, you get 100% visibility into
>      your
>      > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of
>      AppDynamics Pro!
>      >
>      http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>
>      > _______________________________________________
>      > Gmod-schema mailing list
>      > [hidden email]
>      > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>      ------------------------------------------------------------------------------
>      CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>      Learn Why More Businesses Are Choosing CenturyLink Cloud For
>      Critical Workloads, Development Environments & Everything In Between.
>      Get a Quote or Start a Free Trial Today.
>      http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
>      _______________________________________________
>      Gmod-schema mailing list
>      [hidden email]
>      https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>    --
>    Surya Saha
>    Department of Plant Pathology,
>    Cornell University, NY, USA.
>    Sol Genomics Network,
>    Boyce Thompson Institute, Ithaca, NY, USA.
>    http://www.linkedin.com/in/suryasaha
>    Twitter: https://twitter.com/SahaSurya

> ------------------------------------------------------------------------------
> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> Learn Why More Businesses Are Choosing CenturyLink Cloud For
> Critical Workloads, Development Environments & Everything In Between.
> Get a Quote or Start a Free Trial Today.
> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk

> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
CenturyLink Cloud: The Leader in Enterprise Cloud Services.
Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema