Re: [Gmod-gbrowse] No Features When Searching "*"

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Re: [Gmod-gbrowse] No Features When Searching "*"

Scott Cain
Hi Andrew,

I switched over the the schema mailing list.

To load into Chado, try these things:

*  add "ID=ChLG10" to the chromosome line
* completely removing the sequence-region directive couldn't hurt (with it in there, it's a little over specified--I don't remember if the bulk loader would complain about that or not).
* Probably don't use the preprocessor (it looks to me like this file is for a single chromosome (so no splitting) and it looks already sorted).
* Add the --noexon flag when running the bulk loader, since you don't want it to infer the existence of exons from the CDSes, since they are already in the file.

Scott




On Thu, Feb 13, 2014 at 9:33 AM, Andrew Oberlin <[hidden email]> wrote:
Hi Scott,

Thanks for your help! That works for a SeqFeature::Store database. But my next step is to load it into chado. I added an ID=ChLG10 to the comments at the end, which was needed. However, when I go to use the gmod_gff3_preprocessor.pl, I receive the following error:

null value in column "parent" violates not-null constraint

It reports that the occurrence is on the line we have added to the GFF file. I've looked at other GFF files I have that have worked and this line does not look too much different, so I was wondering if you know what this error refers to so I can fix it?

Also, we can possibly move this to the Chado list as well if necessary. 

Again thanks for your help,


Andrew Oberlin





On Wed, Feb 12, 2014 at 1:10 PM, Scott Cain <[hidden email]> wrote:
Hi Andrew,

I added a chromosome line to your GFF:

ChLG10  .       chromosome      1       11386040        .       .       .    Name=ChLG10

And it worked (albeit slowly since I was using the memory adaptor). I think this may be an issue specific to the memory adaptor, because I believe (ie, haven't tested recently) that the sequence-region directive is sufficient for specifying a reference sequence when loading into a database-backed SeqFeature::Store database.


Scott


On Tue, Feb 11, 2014 at 3:49 PM, Andrew Oberlin <[hidden email]> wrote:
Hello all,

I am trying to setup a GBrowse instance using a GFF file located here: 


When I use a simple gff file in the same directory (the volvox remarks gff), GBrowse allows me to search and doesn't give a Not Found error consistently--namely t works fine. But the moment I switch out the gff source to this one, GBrowse cannot find any features when there clearly are some here.

If someone could help me get these to show, it would be much appreciated. Or if someone could point out something about this file specifically that makes GBrowse not work.

Also, for reference I checked the apache error.log and there is no error being thrown and nothing significant when turning on debug in the GBrowse.conf.

Thanks,

Andrew Oberlin

--
Andrew Oberlin
Miami University 2014
Computer Science & Mathematics
[hidden email]  (330) 998-1603

------------------------------------------------------------------------------
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Andrew Oberlin
Miami University 2014
Computer Science & Mathematics
[hidden email]  (330) 998-1603



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
_______________________________________________
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Re: [Gmod-gbrowse] No Features When Searching "*"

Andrew Oberlin
Hi Scott,

I did all of the things you suggested and I got a long print out of errors. But the one I think that is the real problem is:

Unable to find srcfeature ChLG10 in the database.

Do I need to manually add the entry into Chado for a chromosome? I've never had to load a genome for an organism that isn't microbial so I haven't seen these errors before.


Thanks,

Andrew Oberlin



On Thu, Feb 13, 2014 at 12:47 PM, Scott Cain <[hidden email]> wrote:
Hi Andrew,

I switched over the the schema mailing list.

To load into Chado, try these things:

*  add "ID=ChLG10" to the chromosome line
* completely removing the sequence-region directive couldn't hurt (with it in there, it's a little over specified--I don't remember if the bulk loader would complain about that or not).
* Probably don't use the preprocessor (it looks to me like this file is for a single chromosome (so no splitting) and it looks already sorted).
* Add the --noexon flag when running the bulk loader, since you don't want it to infer the existence of exons from the CDSes, since they are already in the file.

Scott




On Thu, Feb 13, 2014 at 9:33 AM, Andrew Oberlin <[hidden email]> wrote:
Hi Scott,

Thanks for your help! That works for a SeqFeature::Store database. But my next step is to load it into chado. I added an ID=ChLG10 to the comments at the end, which was needed. However, when I go to use the gmod_gff3_preprocessor.pl, I receive the following error:

null value in column "parent" violates not-null constraint

It reports that the occurrence is on the line we have added to the GFF file. I've looked at other GFF files I have that have worked and this line does not look too much different, so I was wondering if you know what this error refers to so I can fix it?

Also, we can possibly move this to the Chado list as well if necessary. 

Again thanks for your help,


Andrew Oberlin





On Wed, Feb 12, 2014 at 1:10 PM, Scott Cain <[hidden email]> wrote:
Hi Andrew,

I added a chromosome line to your GFF:

ChLG10  .       chromosome      1       11386040        .       .       .    Name=ChLG10

And it worked (albeit slowly since I was using the memory adaptor). I think this may be an issue specific to the memory adaptor, because I believe (ie, haven't tested recently) that the sequence-region directive is sufficient for specifying a reference sequence when loading into a database-backed SeqFeature::Store database.


Scott


On Tue, Feb 11, 2014 at 3:49 PM, Andrew Oberlin <[hidden email]> wrote:
Hello all,

I am trying to setup a GBrowse instance using a GFF file located here: 


When I use a simple gff file in the same directory (the volvox remarks gff), GBrowse allows me to search and doesn't give a Not Found error consistently--namely t works fine. But the moment I switch out the gff source to this one, GBrowse cannot find any features when there clearly are some here.

If someone could help me get these to show, it would be much appreciated. Or if someone could point out something about this file specifically that makes GBrowse not work.

Also, for reference I checked the apache error.log and there is no error being thrown and nothing significant when turning on debug in the GBrowse.conf.

Thanks,

Andrew Oberlin

--
Andrew Oberlin
Miami University 2014
Computer Science & Mathematics
[hidden email]  (330) 998-1603

------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
_______________________________________________
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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Andrew Oberlin
Miami University 2014
Computer Science & Mathematics
[hidden email]  (330) 998-1603



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Andrew Oberlin
Miami University 2014
Computer Science & Mathematics
[hidden email]  (330) 998-1603

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
_______________________________________________
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Re: [Gmod-gbrowse] No Features When Searching "*"

Scott Cain
Hi Andrew,

Yes, you need a gff line that identifies chromosomes (or whatever the source feature is), something like:

ChLG10   .   chromosome   1   1234567   .   .   .   Name= ChLG10;ID= ChLG10

(The name and ID being the same for the chromosome isn't required by the GFF spec, but Chado will work better if you do that.)

Scott



On Mon, Mar 10, 2014 at 4:57 PM, Andrew Oberlin <[hidden email]> wrote:
Hi Scott,

I did all of the things you suggested and I got a long print out of errors. But the one I think that is the real problem is:

Unable to find srcfeature ChLG10 in the database.

Do I need to manually add the entry into Chado for a chromosome? I've never had to load a genome for an organism that isn't microbial so I haven't seen these errors before.


Thanks,

Andrew Oberlin



On Thu, Feb 13, 2014 at 12:47 PM, Scott Cain <[hidden email]> wrote:
Hi Andrew,

I switched over the the schema mailing list.

To load into Chado, try these things:

*  add "ID=ChLG10" to the chromosome line
* completely removing the sequence-region directive couldn't hurt (with it in there, it's a little over specified--I don't remember if the bulk loader would complain about that or not).
* Probably don't use the preprocessor (it looks to me like this file is for a single chromosome (so no splitting) and it looks already sorted).
* Add the --noexon flag when running the bulk loader, since you don't want it to infer the existence of exons from the CDSes, since they are already in the file.

Scott




On Thu, Feb 13, 2014 at 9:33 AM, Andrew Oberlin <[hidden email]> wrote:
Hi Scott,

Thanks for your help! That works for a SeqFeature::Store database. But my next step is to load it into chado. I added an ID=ChLG10 to the comments at the end, which was needed. However, when I go to use the gmod_gff3_preprocessor.pl, I receive the following error:

null value in column "parent" violates not-null constraint

It reports that the occurrence is on the line we have added to the GFF file. I've looked at other GFF files I have that have worked and this line does not look too much different, so I was wondering if you know what this error refers to so I can fix it?

Also, we can possibly move this to the Chado list as well if necessary. 

Again thanks for your help,


Andrew Oberlin





On Wed, Feb 12, 2014 at 1:10 PM, Scott Cain <[hidden email]> wrote:
Hi Andrew,

I added a chromosome line to your GFF:

ChLG10  .       chromosome      1       11386040        .       .       .    Name=ChLG10

And it worked (albeit slowly since I was using the memory adaptor). I think this may be an issue specific to the memory adaptor, because I believe (ie, haven't tested recently) that the sequence-region directive is sufficient for specifying a reference sequence when loading into a database-backed SeqFeature::Store database.


Scott


On Tue, Feb 11, 2014 at 3:49 PM, Andrew Oberlin <[hidden email]> wrote:
Hello all,

I am trying to setup a GBrowse instance using a GFF file located here: 


When I use a simple gff file in the same directory (the volvox remarks gff), GBrowse allows me to search and doesn't give a Not Found error consistently--namely t works fine. But the moment I switch out the gff source to this one, GBrowse cannot find any features when there clearly are some here.

If someone could help me get these to show, it would be much appreciated. Or if someone could point out something about this file specifically that makes GBrowse not work.

Also, for reference I checked the apache error.log and there is no error being thrown and nothing significant when turning on debug in the GBrowse.conf.

Thanks,

Andrew Oberlin

--
Andrew Oberlin
Miami University 2014
Computer Science & Mathematics
[hidden email]  (330) 998-1603

------------------------------------------------------------------------------
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
http://pubads.g.doubleclick.net/gampad/clk?id=124407151&iu=/4140/ostg.clktrk
_______________________________________________
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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Andrew Oberlin
Miami University 2014
Computer Science & Mathematics
[hidden email]  (330) 998-1603



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Andrew Oberlin
Miami University 2014
Computer Science & Mathematics
[hidden email]  (330) 998-1603



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema