Re: [Gmod-ajax] 0 feature found/no display of data

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Yes, it changed because I refreshed the file. I was saving it at a different place and forgot to refresh it at the other. Stupid
Maybe I address it wrong? I was using http://localhost/jbrowse/ as written in the tutorial, but maybe I have to specify it?

Anja

Date: Fri, 1 Oct 2010 10:43:42 -0700
From: ml-...@n3...
To: fri...@ho...
Subject: Re: 0 features found/no display of data

Ah, OK, things changed; that's good.  The fact that the biodb-to-json script reported that it found 1 feature (which is exactly as many as I would expect it to find), means that everything up to that point appears to be working as expected.  What is happening beyond there I don't know and will punt to Mitch or Ian; my only guess is browser caching causing a problem.

Scott

On Fri, Oct 1, 2010 at 1:28 PM, anja <[hidden email]> wrote:

Hi Scott, 

I used:
anou@anou-laptop:/var/www$ bp_seqfeature_load.pl --d "dbi:Pg:dbname=test" --a DBI::Pg --c taro.gff
loading taro.gff...

98 features loaded in  0.41s                                                    Building object tree... 0.02s
load time:  0.46s
anou@anou-laptop:/var/www$ bin/prepare-refseqs.pl --conf taro.json --refs NC_010109.1

anou@anou-laptop:/var/www$ bin/biodb-to-json.pl --conf taro.json

working on refseq NC_010109.1
working on track nested_tandem_repeat
got 1 features for nested_tandem_repeat

looks alright, doesnt it? By not working I mean that I  dont get to see anything in my browser, only the data I was loading ages ago. Its like it doesnt exist...

Anja

Date: Fri, 1 Oct 2010 10:00:11 -0700

From: [hidden email]
To: [hidden email]

Subject: Re: 0 features found/no display of data

Hi Anja,

This GFF looks OK (though I would suggest giving the top level feature (whose ID is NTR-a) a Name, since JBrowse doesn't use ID values for naming features, but that may not matter).

So, when you say it isn't working, what does that mean?  Is it doing exactly the same thing?  Did you reload the database you were using with the corrected GFF file?

Scott

On Fri, Oct 1, 2010 at 11:19 AM, Anja Friedrich <[hidden email]> wrote:

Hi Scott, 

Thank you
I chose the second way and attached the file again, because it is still not working... Hope I got your substitution advice right?

Anja

Date: Fri, 1 Oct 2010 11:02:04 -0400
Subject: Re: [Gmod-ajax] 0 features found/no display of data
From: [hidden email]

To: [hidden email]

CC: [hidden email]

Hi Anja,

The argument for the prepare-refseqs.pl script is the name of the reference sequence you want prepared.  In your GFF, you sort of have two reference sequences: "NC_010109.1" and "1".  The problem is, NC_010109.1 doesn't have any features on it (it never appears in the first column of the GFF) and 1 is never defined (it doesn't have a gff line with "Name=1" or a sequence-region line).  While this is valid GFF (which is why it successfully loaded in to the SeqFeature::Store database), it doesn't make logical sense.  You can do 1 of two things:

  1. Change the NC_010109.1 to 1 in the sequence-region line then you can supply "1" as an argument for the prepare-refseqs script.

  2.  Substitute NC_010109.1 for 1 in all of the first columns in the whole GFF file and supply "NC_010109.1" to the prepare-refseqs script.

Scott

On Fri, Oct 1, 2010 at 9:29 AM, anja <[hidden email]> wrote:

Hi Scott,

I attached it

Anja

Date: Fri, 1 Oct 2010 06:01:51 -0700
From: [hidden email]

To: [hidden email]
Subject: Re: 0 features found/no display of data

Hi Anja,

It is probably a problem with your GFF.  Since there have been so many

revisions to it, can you remind us what it looks like?

Scott

On Fri, Oct 1, 2010 at 5:10 AM, Anja Friedrich

<[hidden email]> wrote:

> Hi all,

>

> I finally managed to load the data and to run bin/prepare-refseqs.pl

>

> anou@anou-laptop:/var/www$ bp_seqfeature_load.pl --d "dbi:Pg:dbname=test"

> --a DBI::Pg --c taro.gff

> loading taro.gff...

> 98 features loaded in

> 0.20s                                                    Building object

> tree... 0.02s

> load time:  0.23s

> anou@anou-laptop:/var/www$ bin/prepare-refseqs.pl --conf taro.json --refs

> NC_010109.1

> anou@anou-laptop:/var/www$ bin/biodb-to-json.pl --conf taro.json

>

> working on refseq NC_010109.1

> working on track nested_tandem_repeat

> got 0 features for nested_tandem_repeat

>

> But why 0 features? And when I try to see it in the browser I can only see

> the old data I was loading before- like there is no entry of taro...

>

> Anja

>

> ------------------------------------------------------------------------------

> Start uncovering the many advantages of virtual appliances

> and start using them to simplify application deployment and

> accelerate your shift to cloud computing.

> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________

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

>

-- 

------------------------------------------------------------------------

Scott Cain, Ph. D.                                   scott at scottcain dot net

GMOD Coordinator (http://gmod.org/)                     216-392-3087

Ontario Institute for Cancer Research

------------------------------------------------------------------------------

Start uncovering the many advantages of virtual appliances

and start using them to simplify application deployment and