No Details Panel in Gbrowse

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No Details Panel in Gbrowse

Matthew Booker
Hi,

I have spent the last week reviewing everything I can regarding a problem with gbrowse (1.70) not displaying the details panel.

I recently updated my gbrowse mysql database with the release5.28 GFF file. Everything seems to have loaded correctly. However, when I do a search on a gene name or reference sequence range (such as "2L:10000..25000"). I get the multiple matches panel that, in the past, displayed only if two different genes had the same name (which actually happens in the fly world since fly gene names are case sensitive).

So, with "2L:10000...25000", I get this line: "The following 1 regions match your request.". Then there are two links that one can click on "2L:10000..25000
Bio::DB::SeqFeature::Segment" and "2L:10..25 kbp (15 kbp)". If I click on either, I do not get a details image panel, but it just loops back to the same multiple item seach.

Here's what it looks like:
The following 1 regions match your request.
Matches on 2L 
overview_2L
2L:10000..25000Bio::DB::SeqFeature::Segment2L:10..25 kbp (15 kbp)score=n/a


How can I force the details panel to display like gbrowse is supposed to? 

If I click on "Link to Image", a proper image is displayed with the transcripts and genes displayed more or less correctly. This means the data that gbrowse needs for the display is present and gbrowse can find it. 

If you have any ideas, please let me know.

Thanks,
Matt

Matthew Booker
Assistant Director of Screening
Drosophila RNAi Screening Center
77 Ave Louis Pasteur Rm 356
Boston, MA 02115
617-432-6546




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Re: No Details Panel in Gbrowse

Scott Cain
Hi Matthew,

I've never seen behavior like this before; do I understand what you wrote to mean the problems started with an update of your mysql server version?  If that's the case, the obvious quick fix would be to downgrade to an older mysql version.

Is there anything helpful in the error_log?  I'm guessing not from your description of what happens, but it would be good to check.

What happens if use Bio::DB::GFF instead?  I'm guessing there is a subtle bug in the interaction between mysql and Bio::DB::SeqFeature::Store that might be difficult to sort out until we upgrade a mysql server too.

Scott


On Mon, Aug 2, 2010 at 3:28 PM, Matthew Booker <[hidden email]> wrote:
Hi,

I have spent the last week reviewing everything I can regarding a problem with gbrowse (1.70) not displaying the details panel.

I recently updated my gbrowse mysql database with the release5.28 GFF file. Everything seems to have loaded correctly. However, when I do a search on a gene name or reference sequence range (such as "2L:10000..25000"). I get the multiple matches panel that, in the past, displayed only if two different genes had the same name (which actually happens in the fly world since fly gene names are case sensitive).

So, with "2L:10000...25000", I get this line: "The following 1 regions match your request.". Then there are two links that one can click on "2L:10000..25000
Bio::DB::SeqFeature::Segment" and "2L:10..25 kbp (15 kbp)". If I click on either, I do not get a details image panel, but it just loops back to the same multiple item seach.

Here's what it looks like:
The following 1 regions match your request.
Matches on 2L 
overview_2L
2L:10000..25000 Bio::DB::SeqFeature::Segment2L:10..25 kbp (15 kbp) score=n/a


How can I force the details panel to display like gbrowse is supposed to? 

If I click on "Link to Image", a proper image is displayed with the transcripts and genes displayed more or less correctly. This means the data that gbrowse needs for the display is present and gbrowse can find it. 

If you have any ideas, please let me know.

Thanks,
Matt

Matthew Booker
Assistant Director of Screening
Drosophila RNAi Screening Center
77 Ave Louis Pasteur Rm 356
Boston, MA 02115
617-432-6546




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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: No Details Panel in Gbrowse

Matthew Booker-2
Hi Scott,

Thanks for the reply. No, I haven't updated mysql itself. Rather, I loaded a new set of annotations into the gbrowse mysql database, replacing the cold ones (using the -c option bp_seqfeature_load.pl).

I initially tried to use Bio::DB::GFF instead, but had exactly the same problem.

There are no errors in the httpd log file, alas.

Curiously, as bp_seqfeature_load.pl loads, I can see the details panel for the images that have loaded so far. It goes away after a large number of annotation have been loaded. I suspect something in the GFF file is causing the problem, but I have not figured out what.

I didn't create this GFF file; it's downloaded from FlyBase. I've contacted FlyBase and they've been able to help me with a few things, but not with this.

Thanks,
Matt

On Aug 2, 2010, at 4:18 PM, Scott Cain wrote:

Hi Matthew,

I've never seen behavior like this before; do I understand what you wrote to mean the problems started with an update of your mysql server version?  If that's the case, the obvious quick fix would be to downgrade to an older mysql version.

Is there anything helpful in the error_log?  I'm guessing not from your description of what happens, but it would be good to check.

What happens if use Bio::DB::GFF instead?  I'm guessing there is a subtle bug in the interaction between mysql and Bio::DB::SeqFeature::Store that might be difficult to sort out until we upgrade a mysql server too.

Scott


On Mon, Aug 2, 2010 at 3:28 PM, Matthew Booker <[hidden email]> wrote:
Hi,

I have spent the last week reviewing everything I can regarding a problem with gbrowse (1.70) not displaying the details panel.

I recently updated my gbrowse mysql database with the release5.28 GFF file. Everything seems to have loaded correctly. However, when I do a search on a gene name or reference sequence range (such as "2L:10000..25000"). I get the multiple matches panel that, in the past, displayed only if two different genes had the same name (which actually happens in the fly world since fly gene names are case sensitive).

So, with "2L:10000...25000", I get this line: "The following 1 regions match your request.". Then there are two links that one can click on "2L:10000..25000
Bio::DB::SeqFeature::Segment" and "2L:10..25 kbp (15 kbp)". If I click on either, I do not get a details image panel, but it just loops back to the same multiple item seach.

Here's what it looks like:
The following 1 regions match your request.
Matches on 2L 
<image.png>
2L:10000..25000 Bio::DB::SeqFeature::Segment2L:10..25 kbp (15 kbp) score=n/a


How can I force the details panel to display like gbrowse is supposed to? 

If I click on "Link to Image", a proper image is displayed with the transcripts and genes displayed more or less correctly. This means the data that gbrowse needs for the display is present and gbrowse can find it. 

If you have any ideas, please let me know.

Thanks,
Matt

Matthew Booker
Assistant Director of Screening
Drosophila RNAi Screening Center
77 Ave Louis Pasteur Rm 356
Boston, MA 02115
617-432-6546




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------------------------------------------------------------------------
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: No Details Panel in Gbrowse

Josh Goodman

Hi Matt,

Apologies if I've missed this but did you try the two things noted in our
README file
(ftp://ftp.flybase.org/genomes/Drosophila_melanogaster/current/gff/README)?
Namely, removing or modifying all Target and Alias tags that have a value
that is also a chromosome name (e.g. Target=4 or Alias=4) and removing all
chromosome band features with negative coordinates?  Don't forget to
adjust the sequence-region tag.  This sounds a bit like the problem that
these two things can cause.

Cheers,
Josh

On Mon, 2 Aug 2010, Matthew Booker wrote:

> Hi Scott,
> Thanks for the reply. No, I haven't updated mysql itself. Rather, I loaded a new set of annotations into the gbrowse mysql database,
> replacing the cold ones (using the -c option bp_seqfeature_load.pl).
>
> I initially tried to use Bio::DB::GFF instead, but had exactly the same problem.
>
> There are no errors in the httpd log file, alas.
>
> Curiously, as bp_seqfeature_load.pl loads, I can see the details panel for the images that have loaded so far. It goes away after a large
> number of annotation have been loaded. I suspect something in the GFF file is causing the problem, but I have not figured out what.
>
> I didn't create this GFF file; it's downloaded from FlyBase. I've contacted FlyBase and they've been able to help me with a few things, but
> not with this.
>
> Thanks,
> Matt
>
> On Aug 2, 2010, at 4:18 PM, Scott Cain wrote:
>
>       Hi Matthew,
>
>       I've never seen behavior like this before; do I understand what you wrote to mean the problems started with an update of your
>       mysql server version?  If that's the case, the obvious quick fix would be to downgrade to an older mysql version.
>
>       Is there anything helpful in the error_log?  I'm guessing not from your description of what happens, but it would be good to
>       check.
>
>       What happens if use Bio::DB::GFF instead?  I'm guessing there is a subtle bug in the interaction between mysql and
>       Bio::DB::SeqFeature::Store that might be difficult to sort out until we upgrade a mysql server too.
>
>       Scott
>
>
>       On Mon, Aug 2, 2010 at 3:28 PM, Matthew Booker <[hidden email]> wrote:
>             Hi,
> I have spent the last week reviewing everything I can regarding a problem with gbrowse (1.70) not displaying the details panel.
>
> I recently updated my gbrowse mysql database with the release5.28 GFF file. Everything seems to have loaded correctly. However,
> when I do a search on a gene name or reference sequence range (such as "2L:10000..25000"). I get the multiple matches panel
> that, in the past, displayed only if two different genes had the same name (which actually happens in the fly world since fly
> gene names are case sensitive).
>
> So, with "2L:10000...25000", I get this line: "The following 1 regions match your request.". Then there are two links that one
> can click on "2L:10000..25000
> Bio::DB::SeqFeature::Segment" and "2L:10..25 kbp (15 kbp)". If I click on either, I do not get a details image panel, but it
> just loops back to the same multiple item seach.
>
> Here's what it looks like:
> The following 1 regions match your request.
> Matches on 2L 
>                                                                 <image.png>
>
> 2L:10000..25000
> Bio::DB::SeqFeature::Segment
> 2L:10..25 kbp (15 kbp)
> score=n/a
>
>
> How can I force the details panel to display like gbrowse is supposed to? 
>
> If I click on "Link to Image", a proper image is displayed with the transcripts and genes displayed more or less correctly. This
> means the data that gbrowse needs for the display is present and gbrowse can find it. 
>
> If you have any ideas, please let me know.
>
> Thanks,
> Matt
>
> Matthew Booker
> Assistant Director of Screening
> Drosophila RNAi Screening Center
> 77 Ave Louis Pasteur Rm 356
> Boston, MA 02115
> 617-432-6546
> [hidden email]
>
>
>
>
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://p.sf.net/sfu/dev2dev-palm
> _______________________________________________
> 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: No Details Panel in Gbrowse

Josh Goodman
Hi Matt,

I don't know but someone on the gmod-gbrowse list probably does.  Search behavior is very adaptor
dependent so it will depend on the one you are using.  FlyBase uses a custom adaptor so my
experience with our search behavior won't help you any.

Josh

p.s.-I hope you meant chromosome band features and not chromosome arm.

On 08/04/2010 03:28 PM, Matthew Booker wrote:

> Hi Josh,
>
> Thank you for your help. I just removed the chromosome arm features and
> most of the non-FlyBase features and that fixes the problem.
>
> However, I am now having another problem. I can search in gbrowse for
> wingless by typing "wg", and there's no problem. However, if I search by
> FBgn, (FBgn0004009), it won't work. gbrowse appears incapable of
> searching the "ID" attribute.
>
> I added this line to my configuration file:
> search attributes = ID Name Alias Parent Note fullname.
>
> gbrowse successfully searches Name, Alias, and fullname, but won't
> search ID or Parent. Is there anyway I can get gbrowse to search the
> "ID" attribute? I though about editing the GFF file, adding the FBgn as
> an alias, but I hate to have to do that - and I'm leaving my job Friday
> so I'm pressed for time.
>
> -Matt
>
> Matthew Booker
> Assistant Director of Screening
> Drosophila RNAi Screening Center
> 77 Ave Louis Pasteur Rm 356
> Boston, MA 02115
> 617-432-6546
> [hidden email]
>
>

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Re: No Details Panel in Gbrowse

Scott Cain
Hi Matthew,

I haven't had a chance to test this yet, but I think adding "load_id"
to the search attributes list may do the trick.  That is how the ID is
stored in the database.

Scott


On Wed, Aug 4, 2010 at 4:19 PM, Josh Goodman <[hidden email]> wrote:

> Hi Matt,
>
> I don't know but someone on the gmod-gbrowse list probably does.  Search behavior is very adaptor
> dependent so it will depend on the one you are using.  FlyBase uses a custom adaptor so my
> experience with our search behavior won't help you any.
>
> Josh
>
> p.s.-I hope you meant chromosome band features and not chromosome arm.
>
> On 08/04/2010 03:28 PM, Matthew Booker wrote:
>> Hi Josh,
>>
>> Thank you for your help. I just removed the chromosome arm features and
>> most of the non-FlyBase features and that fixes the problem.
>>
>> However, I am now having another problem. I can search in gbrowse for
>> wingless by typing "wg", and there's no problem. However, if I search by
>> FBgn, (FBgn0004009), it won't work. gbrowse appears incapable of
>> searching the "ID" attribute.
>>
>> I added this line to my configuration file:
>> search attributes = ID Name Alias Parent Note fullname.
>>
>> gbrowse successfully searches Name, Alias, and fullname, but won't
>> search ID or Parent. Is there anyway I can get gbrowse to search the
>> "ID" attribute? I though about editing the GFF file, adding the FBgn as
>> an alias, but I hate to have to do that - and I'm leaving my job Friday
>> so I'm pressed for time.
>>
>> -Matt
>>
>> Matthew Booker
>> Assistant Director of Screening
>> Drosophila RNAi Screening Center
>> 77 Ave Louis Pasteur Rm 356
>> Boston, MA 02115
>> 617-432-6546
>> [hidden email]
>>
>>
>
> ------------------------------------------------------------------------------
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> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://p.sf.net/sfu/dev2dev-palm
> _______________________________________________
> 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: No Details Panel in Gbrowse

Matthew Booker
Hi Scott,

That worked! I would *never* have figured that out.

-Matt

Matthew Booker
Assistant Director of Screening
Drosophila RNAi Screening Center
77 Ave Louis Pasteur Rm 356
Boston, MA 02115
617-432-6546
[hidden email]



On Aug 4, 2010, at 4:42 PM, Scott Cain wrote:

> Hi Matthew,
>
> I haven't had a chance to test this yet, but I think adding "load_id"
> to the search attributes list may do the trick.  That is how the ID is
> stored in the database.
>
> Scott
>
>
> On Wed, Aug 4, 2010 at 4:19 PM, Josh Goodman <[hidden email]>  
> wrote:
>> Hi Matt,
>>
>> I don't know but someone on the gmod-gbrowse list probably does.  
>> Search behavior is very adaptor
>> dependent so it will depend on the one you are using.  FlyBase uses  
>> a custom adaptor so my
>> experience with our search behavior won't help you any.
>>
>> Josh
>>
>> p.s.-I hope you meant chromosome band features and not chromosome  
>> arm.
>>
>> On 08/04/2010 03:28 PM, Matthew Booker wrote:
>>> Hi Josh,
>>>
>>> Thank you for your help. I just removed the chromosome arm  
>>> features and
>>> most of the non-FlyBase features and that fixes the problem.
>>>
>>> However, I am now having another problem. I can search in gbrowse  
>>> for
>>> wingless by typing "wg", and there's no problem. However, if I  
>>> search by
>>> FBgn, (FBgn0004009), it won't work. gbrowse appears incapable of
>>> searching the "ID" attribute.
>>>
>>> I added this line to my configuration file:
>>> search attributes = ID Name Alias Parent Note fullname.
>>>
>>> gbrowse successfully searches Name, Alias, and fullname, but won't
>>> search ID or Parent. Is there anyway I can get gbrowse to search the
>>> "ID" attribute? I though about editing the GFF file, adding the  
>>> FBgn as
>>> an alias, but I hate to have to do that - and I'm leaving my job  
>>> Friday
>>> so I'm pressed for time.
>>>
>>> -Matt
>>>
>>> Matthew Booker
>>> Assistant Director of Screening
>>> Drosophila RNAi Screening Center
>>> 77 Ave Louis Pasteur Rm 356
>>> Boston, MA 02115
>>> 617-432-6546
>>> [hidden email]
>>>
>>>
>>
>> ------------------------------------------------------------------------------
>> The Palm PDK Hot Apps Program offers developers who use the
>> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
>> of $1 Million in cash or HP Products. Visit us here for more details:
>> http://p.sf.net/sfu/dev2dev-palm
>> _______________________________________________
>> 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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