gmod-ajax — JBrowse list

Re: [Gmod-ajax] zoom and jbrowse instance

[Mitch S. <mit...@be...>]

  There's not currently a configuration option for this, but it's easy 
to change in the code of your jbrowse instance, on lines 103 and 105 of 
Browser.js:

http://github.com/jbrowse/jbrowse/blob/master/js/Browser.js#L103

You can change the 0.4 and 0.6 to 0 and 1, respectively.

If you're using the 1.1 release zip file from jbrowse.org, then you'll 
have to use index-debug.html to see the change take effect, because the 
regular index.html refers to a minified (compressed) version of the 
javascript.

Hope this helps,
Mitch

On 10/11/2010 07:05 AM, Andrea Malossini wrote:
> Hi,
>
> when creating a jbrowse instance is it possible to show the whole
> genome (chromosome/gene etc) without any zoom by default?
>
> Thanks.
> Andrea
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] Colour reads from a BAM file

[Mitch S. <mit...@be...>]

  The current plan for this is to allow the user to specify a javascript 
function that gets called when features get put on screen, and can 
change the CSS style of a feature based on the feature data (which could 
include the ID, or whatever other information is in the JSON.

I've been experimenting with this lately; for example, in 
ucsc-to-json.pl there's a bit of perl that specifies a javascript 
callback, but it will be possible to specify that on the command line 
for flatfile-to-json.pl or in a config file for biodb-to-json.pl:

==========
     my $color = sprintf("#%02x%02x%02x",
                         $track->{colorR},
                         $track->{colorG},
                         $track->{colorB});

     if ($subfeatures) {
         $style{subfeatureHeaders} = \@subfeatHeaders;
         $style{class} = "generic_parent";
         $style{clientConfig}->{featureCallback} = <<ENDJS;
function(feat, fields, div) {
     if (fields.type) {
         div.className = "basic";
         switch (feat[fields.type]) {
         case "CDS":
         case "thick":
             div.style.height = "10px";
             div.style.marginTop = "-3px";
             break;
         case "UTR":
         case "thin":
             div.style.height = "6px";
             div.style.marginTop = "-1px";
             break;
         }
         div.style.backgroundColor = "$color";
     }
}
ENDJS
     }
==========

Currently, the callback gets the feature data, the "fields" object that 
specifies what's in the feature data, and the actual HTML element that 
will represent the feature.  That's not necessarily the final interface, 
but it's what I'm currently experimenting with.

This option should make it into the next release in December, but for 
now it's just work-in-progress.  On the plus side, if you have opinions 
about how it should work, now's your chance to weigh in :)

Mitch

On 10/08/2010 04:09 AM, James Casbon wrote:
> I'd like to see this as well.  My preference would be to assign
> colours based on the read group annotations in the BAM file.
>
> On 8 October 2010 11:52, James Morris<jm...@sa...>  wrote:
>> Hello,
>>
>> I am using Jbrowse to view some RNAseq data just on my local machine.
>>
>> Is it possible to colour the reads in a single track differently based on information I have in the id.
>>
>> I have 256 different classes (based on a 4bp sequence) so simply creating separate tracks for each class would not work as there would be too many tracks to view at once.
>>
>> If I could colour the reads I think it will be easy to visualise the distribution of the different classes at points where the reads pileup.
>>
>> Any help on this would be great.
>>
>> Thanks,
>>
>> James
>>
>> --
>>   The Wellcome Trust Sanger Institute is operated by Genome Research
>>   Limited, a charity registered in England with number 1021457 and a
>>   company registered in England with number 2742969, whose registered
>>   office is 215 Euston Road, London, NW1 2BE.
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
>> Spend less time writing and  rewriting code and more time creating great
>> experiences on the web. Be a part of the beta today.
>> http://p.sf.net/sfu/beautyoftheweb
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] UCSC to Jbrowse adaptor

[Mitch S. <mit...@be...>]

  I checked in bin/ucsc-to-json.pl on the "jsongen-refactor" branch:

http://github.com/jbrowse/jbrowse/tree/jsongen-refactor

That branch is still very much a work in progress; flatfile-to-json.pl 
and biodb-to-json.pl currently don't work on the branch (they do in 
master, just not in jsongen-refactor).

There has already been one JSON format change on that branch, and there 
will be more; the program names may change, the command line arguments 
may change, it's not well documented, etc.  In other words, here be 
dragons!  But I said I'd send a message when I checked it in, so here 
you go.

The way I've been using it is:

$ rsync -ahvzP --exclude="chain*" --exclude="net*" 
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ 
~/data/ucsc/hg19/database

$ bin/ucsc-to-json.pl --in ~/data/ucsc/hg19/database --track "YRI NA18507"

where the --in parameter is the directory with the downloaded annotation 
database dumps from UCSC, and the --track parameter is the shortLabel of 
the track (the second column in trackDb.txt.gz).

As for whether or not it would be hard to write something for Ensembl, I 
really don't know.  Looking at their data is on my to-do list, but I'm 
not very familiar with what they provide.

Mitch

On 10/11/2010 04:09 AM, Mitch Skinner wrote:
>  There are still a few bugs in it; it's only a few days old, and I 
> haven't checked it in, yet.  I'll send a message to the list when I 
> do, probably on Monday or Tuesday.
>
> It currently only supports "bed" and "genePred" tables; psl, bedGraph, 
> and wiggle tables are still to-do.  I'm not sure how important the 
> other types (chain, netAlign, ctgPos, expRatio, rmsk, wigMaf) are for 
> JBrowse.
>
> The current version pulls directly from UCSC's public mysql instance; 
> I'm a little worried that they'll be unhappy with that.  I don't think 
> it's all that rough on the mysql server, though.  The script spends 
> most of its time processing the data on the client, and writing out 
> the JBrowse JSON.  So it's not sending queries terribly frequently.  
> Some of the queries it does make can pull out large amounts of data, 
> though.
>
> Mitch
>
> On 10/11/2010 03:00 AM, James Morris wrote:
>> Hello,
>>
>> I saw on the blog that you now have a UCSC to Jbrowse adaptor, this 
>> sounds great!
>>
>> Is this code available to test? I had a look on git hub but could not 
>> see anything obvious.
>>
>> Thanks,
>>
>> James
>>
>

[Gmod-ajax] Did a "git reset" on the JBrowse git repository

[Mitch S. <mit...@be...>]

  The week before last, some things got committed to the JBrowse master 
branch that were meant for a development branch.  I just undid those 
changes and pushed the undoing to github.  I don't expect this to affect 
very many people; it only affects people using git (so it won't affect 
you if you downloaded JBrowse as a zip or tar file).  Just in case, 
though, what follows is everything I know about how this might affect you.

If you've been following JBrowse using git, then this will only affect 
you if:

A. you have local changes/commits (is anyone doing this?), or
B. if your git repo is more up to date than September 26th (i.e., if 
you've done a "git clone" or a "git pull" since then)

If you do a "git pull", followed by "git status", and get a message that 
says "Your branch is ahead of 'origin/master' by" some number of 
commits, you can get back in sync with upstream jbrowse by doing this:

$ git reset --hard origin/master

If you have local changes, this will appear to get rid of them.  If you 
want to keep those changes, then:

1. first of all, make a copy of your local repo before you do anything 
to it, just in case.

2. before the "git reset", make sure your changes are committed, and 
that you know the commit IDs.  You can do this by doing a "git log" and 
making a note of the commit IDs (sha1 hashes) of your commits.

3. after the "git reset", do a "git cherry-pick" with the commit IDs 
from step 2.  This will apply your changes again.

If you run into trouble with this, please let me know and I'll do what I 
can to help straighten things out.

Regards,
Mitch

On 10/01/2010 12:16 AM, Mitch Skinner wrote:
>  There were some things that were supposed to be committed to a 
> development branch, that accidentally got committed to the master 
> branch.  Those changes included a merge, and undoing a merge is 
> apparently not a completely simple thing with git[1], and I'm still 
> figuring out how it should be done.
>
> For right now, you can fix the problem by going back to an earlier 
> revision like this:
>
> $ git checkout 9a1542d7f80cb3836b49f6b72df2628888d38292
>
> and you'll probably want to avoid doing a "git pull" until we revert 
> those changes.
>
> Mitch
>
> [1] 
> http://www.kernel.org/pub/software/scm/git/docs/howto/revert-a-faulty-merge.txt
>
> On 09/30/2010 10:03 PM, Joseph Pickrell wrote:
>> Hi all,
>>
>> I'm new to JBrowse, and, after following the tutorial, set up the test
>> (Volvox) database here:
>> http://www.genomesunzipped.org/jbrowse-jbrowse-b24b842/
>>
>> When viewing this page with Firefox (3.6.1), everything looks great.
>> However, when viewing it with Safari (5.0.2) or Chrome (6.0.472.63,
>> all on OS X), I can't drag any of the track names on to the display
>> (or rather, I can drag them, but not drop them). The demo browsers
>> (eg. drosophila) look fine.
>>
>> Any suggestions?
>>
>> Thanks,
>>
>> Joe Pickrell
>>
>> ------------------------------------------------------------------------------ 
>>
>> 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
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Fwd: JBrowse: Strange peaks appear in WIG tracks

[David B. <dav...@gm...>]

Thank you very much Ian.

On Tue, Oct 12, 2010 at 1:38 AM, Ian Holmes <ih...@be...> wrote:

> Thanks David. I just committed a fix and closed the ticket. Best wishes,
> Ian
>
> David Breimann wrote:
>
>>
>> The files are attached again. I hope you'd be able to recreate and solve
>> the issue.
>>
>> Thanks,
>> Dave
>>
>>
>> ---------- Forwarded message ----------
>> From: *David Breimann* <dav...@gm... <mailto:
>> dav...@gm...>>
>> Date: Wed, Oct 6, 2010 at 10:59 PM
>> Subject: JBrowse: Strange peaks appear in WIG tracks
>> To: Mitch Skinner <mit...@be... <mailto:
>> mit...@be...>>
>> Cc: Ian Holmes <ih...@be... <mailto:ih...@be...>>
>>
>>
>> Hi Mitch,
>>
>> I didn't send this to the mailing list to avoid sharing the large files
>> with everyone, but feel free to cc your reply to the list.
>>
>> I've encountered a strange phenomena: some peaks appear in tracks created
>> from WIG files with no apparent reason. The WIG doesn't have any value that
>> supports a "peak" in those positions.
>>
>> Recreate the situation:
>> * start with a clean JBrowse clone.
>> * prepare-refseq with the attached fasta file (in the archive).
>> * wig-to-json with the attached WIG file (in the archive).
>> * Now zoom in to position 68000. Attached is a print-screen of what I see.
>> Inspect the WIG and see all the values at this area are 2-3 and there's no
>> peak.
>>
>> Keep up the good work!
>> Dave
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>>

Re: [Gmod-ajax] Fwd: JBrowse: Strange peaks appear in WIG tracks

[Ian H. <ih...@be...>]

Thanks David. I just committed a fix and closed the ticket. Best wishes, Ian

David Breimann wrote:
> 
> The files are attached again. I hope you'd be able to recreate and solve 
> the issue.
> 
> Thanks,
> Dave
> 
> 
> ---------- Forwarded message ----------
> From: *David Breimann* <dav...@gm... 
> <mailto:dav...@gm...>>
> Date: Wed, Oct 6, 2010 at 10:59 PM
> Subject: JBrowse: Strange peaks appear in WIG tracks
> To: Mitch Skinner <mit...@be... 
> <mailto:mit...@be...>>
> Cc: Ian Holmes <ih...@be... <mailto:ih...@be...>>
> 
> 
> Hi Mitch,
> 
> I didn't send this to the mailing list to avoid sharing the large files 
> with everyone, but feel free to cc your reply to the list.
> 
> I've encountered a strange phenomena: some peaks appear in tracks 
> created from WIG files with no apparent reason. The WIG doesn't have any 
> value that supports a "peak" in those positions.
> 
> Recreate the situation:
> * start with a clean JBrowse clone.
> * prepare-refseq with the attached fasta file (in the archive).
> * wig-to-json with the attached WIG file (in the archive).
> * Now zoom in to position 68000. Attached is a print-screen of what I 
> see. Inspect the WIG and see all the values at this area are 2-3 and 
> there's no peak.
> 
> Keep up the good work!
> Dave
> 
> 
> 
> ------------------------------------------------------------------------
> 

Re: [Gmod-ajax] JBrowse: Strange peaks appear in WIG tracks

[Ian H. <ih...@be...>]

PS, I believe all we will really need is the WIG file
If you can re-send this I will try to fix it today
Best, Ian

On 10/11/10 10:44 AM, Ian Holmes wrote:
> Hi David,
>
> We did receive your email - thanks.
>
> There is actually a lighthouse ticket for this issue already, though it
> is somewhat cryptic:
>
> http://jbrowse.lighthouseapp.com/projects/23792/tickets/19-handle-wiggle-regions-that-span-tile-boundaries
>
> If you get a chance, it'd be great if you could post your files for
> recreating the issue as a comment/footnote to this ticket (I would do
> this myself but I seem to have misplaced your original email unfortunately)
>
> Best wishes
> Ian
>
>
>
> On 10/11/10 4:41 AM, David Breimann wrote:
>> Hello again,
>>
>> I just wanted to verify you have received this email.
>>
>> Best,
>> Dave
>>
>> On Wed, Oct 6, 2010 at 10:59 PM, David Breimann<dav...@gm...>wrote:
>>
>>> Hi Mitch,
>>>
>>> I didn't send this to the mailing list to avoid sharing the large files
>>> with everyone, but feel free to cc your reply to the list.
>>>
>>> I've encountered a strange phenomena: some peaks appear in tracks created
>>> from WIG files with no apparent reason. The WIG doesn't have any value that
>>> supports a "peak" in those positions.
>>>
>>> Recreate the situation:
>>> * start with a clean JBrowse clone.
>>> * prepare-refseq with the attached fasta file (in the archive).
>>> * wig-to-json with the attached WIG file (in the archive).
>>> * Now zoom in to position 68000. Attached is a print-screen of what I see.
>>> Inspect the WIG and see all the values at this area are 2-3 and there's no
>>> peak.
>>>
>>> Keep up the good work!
>>> Dave
>>>
>>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] JBrowse: Strange peaks appear in WIG tracks

[Ian H. <ih...@be...>]

Hi David,

We did receive your email - thanks.

There is actually a lighthouse ticket for this issue already, though it 
is somewhat cryptic:

http://jbrowse.lighthouseapp.com/projects/23792/tickets/19-handle-wiggle-regions-that-span-tile-boundaries

If you get a chance, it'd be great if you could post your files for 
recreating the issue as a comment/footnote to this ticket (I would do 
this myself but I seem to have misplaced your original email unfortunately)

Best wishes
Ian



On 10/11/10 4:41 AM, David Breimann wrote:
> Hello again,
>
> I just wanted to verify you have received this email.
>
> Best,
> Dave
>
> On Wed, Oct 6, 2010 at 10:59 PM, David Breimann<dav...@gm...>wrote:
>
>> Hi Mitch,
>>
>> I didn't send this to the mailing list to avoid sharing the large files
>> with everyone, but feel free to cc your reply to the list.
>>
>> I've encountered a strange phenomena: some peaks appear in tracks created
>> from WIG files with no apparent reason. The WIG doesn't have any value that
>> supports a "peak" in those positions.
>>
>> Recreate the situation:
>> * start with a clean JBrowse clone.
>> * prepare-refseq with the attached fasta file (in the archive).
>> * wig-to-json with the attached WIG file (in the archive).
>> * Now zoom in to position 68000. Attached is a print-screen of what I see.
>> Inspect the WIG and see all the values at this area are 2-3 and there's no
>> peak.
>>
>> Keep up the good work!
>> Dave
>>
>

[Gmod-ajax] zoom and jbrowse instance

[Andrea M. <and...@un...>]

Hi,

when creating a jbrowse instance is it possible to show the whole
genome (chromosome/gene etc) without any zoom by default?

Thanks.
Andrea

Re: [Gmod-ajax] UCSC to Jbrowse adaptor

[Mitch S. <mit...@be...>]

  There are still a few bugs in it; it's only a few days old, and I 
haven't checked it in, yet.  I'll send a message to the list when I do, 
probably on Monday or Tuesday.

It currently only supports "bed" and "genePred" tables; psl, bedGraph, 
and wiggle tables are still to-do.  I'm not sure how important the other 
types (chain, netAlign, ctgPos, expRatio, rmsk, wigMaf) are for JBrowse.

The current version pulls directly from UCSC's public mysql instance; 
I'm a little worried that they'll be unhappy with that.  I don't think 
it's all that rough on the mysql server, though.  The script spends most 
of its time processing the data on the client, and writing out the 
JBrowse JSON.  So it's not sending queries terribly frequently.  Some of 
the queries it does make can pull out large amounts of data, though.

Mitch

On 10/11/2010 03:00 AM, James Morris wrote:
> Hello,
>
> I saw on the blog that you now have a UCSC to Jbrowse adaptor, this sounds great!
>
> Is this code available to test? I had a look on git hub but could not see anything obvious.
>
> Thanks,
>
> James
>

[Gmod-ajax] UCSC to Jbrowse adaptor

[James M. <jm...@sa...>]

Hello,

I saw on the blog that you now have a UCSC to Jbrowse adaptor, this sounds great!

Is this code available to test? I had a look on git hub but could not see anything obvious.

Thanks,

James

-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

Re: [Gmod-ajax] Colour reads from a BAM file

[James C. <ca...@gm...>]

I'd like to see this as well.  My preference would be to assign
colours based on the read group annotations in the BAM file.

On 8 October 2010 11:52, James Morris <jm...@sa...> wrote:
> Hello,
>
> I am using Jbrowse to view some RNAseq data just on my local machine.
>
> Is it possible to colour the reads in a single track differently based on information I have in the id.
>
> I have 256 different classes (based on a 4bp sequence) so simply creating separate tracks for each class would not work as there would be too many tracks to view at once.
>
> If I could colour the reads I think it will be easy to visualise the distribution of the different classes at points where the reads pileup.
>
> Any help on this would be great.
>
> Thanks,
>
> James
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Colour reads from a BAM file

[James M. <jm...@sa...>]

Hello,

I am using Jbrowse to view some RNAseq data just on my local machine.

Is it possible to colour the reads in a single track differently based on information I have in the id. 

I have 256 different classes (based on a 4bp sequence) so simply creating separate tracks for each class would not work as there would be too many tracks to view at once.

If I could colour the reads I think it will be easy to visualise the distribution of the different classes at points where the reads pileup.

Any help on this would be great.

Thanks,

James

-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

[Mitch S. <cra...@ar...>]

  On 10/06/2010 05:14 AM, anja wrote:
> sent

I haven't received it; it might be too large to email.  If you can put 
it online (this is your eventual goal, right?) then I could look to see 
what's going on.  Otherwise, you can compare your setup to mine and see 
what the differences are.

> There is something else I noticed by looking at your visualisation. 
> For example are the first 3 variants small, but have the same size as 
> a tall motif. The second tall motif is not displayed, there is just 
> the grey line... What can be the reason for this?

It's a typo in your CSS; the second tall motif is being displayed at the 
beginning, making the first 3 variants look tall.  The second tall motif 
is a "tall purple" one, and in the CSS there's this:

=====
.tall_blue,
.tall_purple
.tall_red,
=====

That missing comma for tall_purple is what's causing it.

Mitch

[Gmod-ajax] FW: data are not displayed even though they were loaded (JBrowse)

[Anja F. <fri...@ho...>]

From: fri...@ho...
To: cra...@ar...
Subject: RE: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)
Date: Wed, 6 Oct 2010 22:31:56 +0200








upload here

http://www.file-upload.net/download-2871690/taro.tar.gz.html

Anja


> Date: Wed, 6 Oct 2010 13:08:33 -0700
> From: cra...@ar...
> To: fri...@ho...
> CC: gmo...@li...
> Subject: Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)
> 
>   On 10/06/2010 05:14 AM, anja wrote:
> > sent
> 
> I haven't received it; it might be too large to email.  If you can put 
> it online (this is your eventual goal, right?) then I could look to see 
> what's going on.  Otherwise, you can compare your setup to mine and see 
> what the differences are.
> 
> > There is something else I noticed by looking at your visualisation. 
> > For example are the first 3 variants small, but have the same size as 
> > a tall motif. The second tall motif is not displayed, there is just 
> > the grey line... What can be the reason for this?
> 
> It's a typo in your CSS; the second tall motif is being displayed at the 
> beginning, making the first 3 variants look tall.  The second tall motif 
> is a "tall purple" one, and in the CSS there's this:
> 
> =====
> .tall_blue,
> .tall_purple
> .tall_red,
> =====
> 
> That missing comma for tall_purple is what's causing it.
> 
> Mitch
> 
 		 	   		  

[Gmod-ajax] Display gene names in JBrowse?

[Joseph P. <joe...@gm...>]

Hi all,

I have a .gff file of transcripts with the gene names listed as
aliases, for example:
chr21   UCSC_1  mRNA    37714471        37809548        .       +
 .       ID=NM_130437;Alias=DYRK1A

I'd like to display the gene name somewhere, rather than the ID. In
GBrowse, I'd put this in the description, eg.,
description  = sub {
        my $f = shift;
        return $f->attributes('Alias');
        }

In JBrowse, I can't seem to find anything like this. Is this possible?

Thanks,

Joe Pickrell

Re: [Gmod-ajax] speed up biodb-to-json.pl?

[Joseph P. <joe...@gm...>]

Thanks. I tried loading from .bed flatfiles, and it seems to be much
faster. It's possible this was a memory issue; I'm running a small EC2
instance (with 1.7G), and it might have been swapping, or whatever the
equivalent is for an EC2, without me realizing.

Thanks again,

Joe

On Tue, Oct 5, 2010 at 7:30 PM, Mitch Skinner
<mit...@be...> wrote:
>  I've loaded up dbSNP once in our hg19 demo (which, unfortunately, is
> currently offline due to a hard drive crash), and I don't think it took
> anywhere near that long.  In that case, I used flatfile-to-json.pl with a
> BED file data source, though.  flatfile-to-json.pl doesn't currently handle
> large GFF files well, but it can handle dbSNP-sized BED files okay.  It
> helps to run it a chromosome at a time, though.
>
> If you run "top" on the machine, is it spending a lot of time in iowait?  Is
> mysql using a lot of CPU?  Is it swapping?  How much RAM does the machine
> have?
>
> I'm currently doing some work to speed this up, and make it use less RAM;
> that work should make it into the next release in December.
>
> Mitch
>
> On 10/05/2010 07:10 AM, Joseph Pickrell wrote:
>>
>> Hi all,
>>
>> I've loaded human dbSNP (11 million features) into a SeqFeature
>> database, and am trying to run biodb-to-json.pl. It appears this is
>> going to take quite a long time on my web server (it's been going for
>> a couple days now, and is still processing chromosome 1). Is there a
>> way to speed this up? For example, is flatfile-to-json faster? Or
>> could I run it on my cluster, and then transfer over the files? If so,
>> which files are the key ones to transfer?
>>
>> Has anyone else tried anything along these lines?
>>
>> Thanks,
>>
>> Joe Pickrell
>>
>>
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
>> Spend less time writing and  rewriting code and more time creating great
>> experiences on the web. Be a part of the beta today.
>> http://p.sf.net/sfu/beautyoftheweb
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>

Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

[anja <fri...@ho...>]

sent
There is something else I noticed by looking at your visualisation. For example are the first 3 variants small, but have the same size as a tall motif. The second tall motif is not displayed, there is just the grey line... What can be the reason for this?

Anja

Date: Wed, 6 Oct 2010 05:09:33 -0700
From: ml-...@n3...
To: fri...@ho...
Subject: Re: data are not displayed even though they were loaded (JBrowse)





  
    
  
  
    It has to be close.  Do this:

    

    cd /var/www

    tar czf taro.tar.gz *

    

    and send me the taro.tar.gz.

    

    Mitch

    

    On 10/06/2010 04:59 AM, anja wrote:
    
      yes

      

      Date: Wed, 6 Oct 2010 04:56:55 -0700

      From: [hidden email]

      To: [hidden email]

      Subject: Re: data are not displayed even though they were loaded
      (JBrowse)

      

      The genome-2.css file is in /var/www?

      

      On 10/06/2010 04:51 AM, anja wrote:
       fixed
        everything but now I have a blank page...

        

        Anja

        

        Date: Wed, 6 Oct 2010 04:33:30 -0700

        From: [hidden email]

        To: [hidden email]

        Subject: Re: data are not displayed even though they were loaded
        (JBrowse)

        

        Hmmm, I know that we're very close, I tried out the data from
        your taro-tracks.tar.gz:

        

        http://jbrowse.org/test/anja/?loc=NC_010109.1:939..2254&tracks=DNA,nested_tandem_repeat

        

        I noticed two things when I was setting that up; one was that
        the CSS file that you sent was named genome-2.css.  The
        index.html file has to refer to the correct CSS file.  In the
        index.html file, there's a line like this:

        

            <link rel="stylesheet" type="text/css"
        href="genome.css"></link>

        

        I put your genome-2.css file in the same directory as the
        original genome.css, and changed that line in index.html to:

        

            <link rel="stylesheet" type="text/css"
        href="genome-2.css"></link>

        

        Also, in the CSS file you sent, there was a line like this:

        

            .minus-tall_orange, {

        

        which has an extra comma; it shouldn't have that comma at the
        end, like this:

        

            .minus-tall_orange {

        

        or, if the data is unstranded, it should look like this:

        

            .tall_orange {

        

        

        Also, some of the CSS classes were missing the "." at the
        beginning.

        

        Mitch

        

        

        

        On 10/06/2010 12:43 AM, Anja Friedrich wrote:
         Thank
          you very much for your time and help.

          I was afraid something like this will happen when I change it.
          But as I don't know whether they are stranded or not, I
          thought its better to mark it as unknown...

          I changed all the classes but it still won't display the
          motifs. Do I have to change it somewhere in addition?

          

          Anja

          Date: Tue, 5 Oct 2010 18:31:31 -0700

          From: [hidden
            email]

          To: [hidden
            email]; [hidden
            email]

          Subject: Re: [Gmod-ajax] data are not displayed even though
          they were loaded (JBrowse)

          

          Okay, one of the GFF files that you sent earlier had strand
          information for the motifs.  I didn't notice that your later
          GFF files listed the motifs as being unstranded.

          

          That's why, in the CSS example I sent earlier, the CSS classes
          were all listed with separate "plus-" and "minus-" versions.

          

          If the motifs don't have strand information, then the CSS file
          should have CSS class names without those "plus-" and "minus-"
          prefixes.  For example, in the earlier example CSS file I
          sent, I had this:

          

          =====

          .plus-small_red,

          .plus-small_blue,

          .plus-small_purple,

          .plus-tall_blue,

          .plus-tall_purple,

          .minus-small_red,

          .minus-small_blue,

          .minus-small_purple,

          .minus-tall_blue,

          .minus-tall_purple {

              position: absolute;

              cursor: pointer;

              z-index: 10;

              min-width: 1px;

          }

          

          .plus-small_red, .minus-small_red {

              background-color: #EB2A2A; height: 6px; margin-top: -1px;

          }

          .plus-small_blue, .minus-small_blue {

              background-color: #46A1E0; height: 6px; margin-top: -1px;

          }

          .plus-small_purple, .minus-small_purple {

              background-color: #7322BF; height: 6px; margin-top: -1px;

          }

          .plus-tall_blue, .minus-tall_blue {

              background-color: #46A1E0; height: 10px; margin-top: -3px;

          }

          .plus-tall_purple, .minus-tall_purple {

              background-color: #7322BF; height: 10px; margin-top: -3px;

          }

          =====

          

          

          but if your motifs are unstranded, you could have this
          instead:

          

          

          =====

          .small_red,

          .small_blue,

          .small_purple,

          .tall_blue,

          .tall_purple {

              position: absolute;

              cursor: pointer;

              z-index: 10;

              min-width: 1px;

          }

          

          .small_red {

              background-color: #EB2A2A; height: 6px; margin-top: -1px;

          }

          .small_blue {

              background-color: #46A1E0; height: 6px; margin-top: -1px;

          }

          .small_purple {

              background-color: #7322BF; height: 6px; margin-top: -1px;

          }

          .tall_blue {

              background-color: #46A1E0; height: 10px; margin-top: -3px;

          }

          .tall_purple {

              background-color: #7322BF; height: 10px; margin-top: -3px;

          }

          =====

          

          

          Or, if your data has both stranded and unstranded features,
          you could include both stranded and unstranded versions of
          your CSS classes.

          

          Mitch

          

          On 10/05/2010 03:39 PM, Anja Friedrich wrote:
           done

            

            > Date: Tue, 5 Oct 2010 15:37:01 -0700

            > From: [hidden
              email]

            > To: [hidden
              email]; [hidden
              email]

            > Subject: Re: [Gmod-ajax] data are not displayed even
            though they were loaded (JBrowse)

            > 

            > Can you do this:

            > 

            > cd /var/www

            > tar czf taro-tracks.tar.gz data/tracks

            > 

            > That will create a file named taro-tracks.tar.gz, with
            your generated 

            > data. Then can you email the file to me? That should
            help me figure 

            > out what's going on.

            > 

            > Mitch

            > 

          
          

          
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Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

[Mitch S. <mit...@be...>]

  It has to be close.  Do this:

cd /var/www
tar czf taro.tar.gz *

and send me the taro.tar.gz.

Mitch

On 10/06/2010 04:59 AM, anja wrote:
> yes
>
> ------------------------------------------------------------------------
> Date: Wed, 6 Oct 2010 04:56:55 -0700
> From: [hidden email] </user/SendEmail.jtp?type=node&node=1641991&i=0>
> To: [hidden email] </user/SendEmail.jtp?type=node&node=1641991&i=1>
> Subject: Re: data are not displayed even though they were loaded (JBrowse)
>
> The genome-2.css file is in /var/www?
>
> On 10/06/2010 04:51 AM, anja wrote:
>
>     fixed everything but now I have a blank page...
>
>     Anja
>
>     ------------------------------------------------------------------------
>     Date: Wed, 6 Oct 2010 04:33:30 -0700
>     From: [hidden email]
>     <http:///user/SendEmail.jtp?type=node&node=1641965&i=0&by-user=t>
>     To: [hidden email]
>     <http:///user/SendEmail.jtp?type=node&node=1641965&i=1&by-user=t>
>     Subject: Re: data are not displayed even though they were loaded
>     (JBrowse)
>
>     Hmmm, I know that we're very close, I tried out the data from your
>     taro-tracks.tar.gz:
>
>     http://jbrowse.org/test/anja/?loc=NC_010109.1:939..2254&tracks=DNA,nested_tandem_repeat
>     <http://jbrowse.org/test/anja/?loc=NC_010109.1:939..2254&tracks=DNA,nested_tandem_repeat>
>
>     I noticed two things when I was setting that up; one was that the
>     CSS file that you sent was named genome-2.css.  The index.html
>     file has to refer to the correct CSS file.  In the index.html
>     file, there's a line like this:
>
>     <link rel="stylesheet" type="text/css" href="genome.css"></link>
>
>     I put your genome-2.css file in the same directory as the original
>     genome.css, and changed that line in index.html to:
>
>     <link rel="stylesheet" type="text/css" href="genome-2.css"></link>
>
>     Also, in the CSS file you sent, there was a line like this:
>
>         .minus-tall_orange, {
>
>     which has an extra comma; it shouldn't have that comma at the end,
>     like this:
>
>         .minus-tall_orange {
>
>     or, if the data is unstranded, it should look like this:
>
>         .tall_orange {
>
>
>     Also, some of the CSS classes were missing the "." at the beginning.
>
>     Mitch
>
>
>
>     On 10/06/2010 12:43 AM, Anja Friedrich wrote:
>
>         Thank you very much for your time and help.
>         I was afraid something like this will happen when I change it.
>         But as I don't know whether they are stranded or not, I
>         thought its better to mark it as unknown...
>         I changed all the classes but it still won't display the
>         motifs. Do I have to change it somewhere in addition?
>
>         Anja
>         ------------------------------------------------------------------------
>         Date: Tue, 5 Oct 2010 18:31:31 -0700
>         From: [hidden email]
>         <http:///user/SendEmail.jtp?type=node&node=1641912&i=0>
>         To: [hidden email]
>         <http:///user/SendEmail.jtp?type=node&node=1641912&i=1>;
>         [hidden email]
>         <http:///user/SendEmail.jtp?type=node&node=1641912&i=2>
>         Subject: Re: [Gmod-ajax] data are not displayed even though
>         they were loaded (JBrowse)
>
>         Okay, one of the GFF files that you sent earlier had strand
>         information for the motifs.  I didn't notice that your later
>         GFF files listed the motifs as being unstranded.
>
>         That's why, in the CSS example I sent earlier, the CSS classes
>         were all listed with separate "plus-" and "minus-" versions.
>
>         If the motifs don't have strand information, then the CSS file
>         should have CSS class names without those "plus-" and "minus-"
>         prefixes.  For example, in the earlier example CSS file I
>         sent, I had this:
>
>         =====
>         .plus-small_red,
>         .plus-small_blue,
>         .plus-small_purple,
>         .plus-tall_blue,
>         .plus-tall_purple,
>         .minus-small_red,
>         .minus-small_blue,
>         .minus-small_purple,
>         .minus-tall_blue,
>         .minus-tall_purple {
>             position: absolute;
>             cursor: pointer;
>             z-index: 10;
>             min-width: 1px;
>         }
>
>         .plus-small_red, .minus-small_red {
>             background-color: #EB2A2A; height: 6px; margin-top: -1px;
>         }
>         .plus-small_blue, .minus-small_blue {
>             background-color: #46A1E0; height: 6px; margin-top: -1px;
>         }
>         .plus-small_purple, .minus-small_purple {
>             background-color: #7322BF; height: 6px; margin-top: -1px;
>         }
>         .plus-tall_blue, .minus-tall_blue {
>             background-color: #46A1E0; height: 10px; margin-top: -3px;
>         }
>         .plus-tall_purple, .minus-tall_purple {
>             background-color: #7322BF; height: 10px; margin-top: -3px;
>         }
>         =====
>
>
>         but if your motifs are unstranded, you could have this instead:
>
>
>         =====
>         .small_red,
>         .small_blue,
>         .small_purple,
>         .tall_blue,
>         .tall_purple {
>             position: absolute;
>             cursor: pointer;
>             z-index: 10;
>             min-width: 1px;
>         }
>
>         .small_red {
>             background-color: #EB2A2A; height: 6px; margin-top: -1px;
>         }
>         .small_blue {
>             background-color: #46A1E0; height: 6px; margin-top: -1px;
>         }
>         .small_purple {
>             background-color: #7322BF; height: 6px; margin-top: -1px;
>         }
>         .tall_blue {
>             background-color: #46A1E0; height: 10px; margin-top: -3px;
>         }
>         .tall_purple {
>             background-color: #7322BF; height: 10px; margin-top: -3px;
>         }
>         =====
>
>
>         Or, if your data has both stranded and unstranded features,
>         you could include both stranded and unstranded versions of
>         your CSS classes.
>
>         Mitch
>
>         On 10/05/2010 03:39 PM, Anja Friedrich wrote:
>
>             done
>
>             > Date: Tue, 5 Oct 2010 15:37:01 -0700
>             > From: [hidden email]
>             <http:///user/SendEmail.jtp?type=node&node=1641912&i=3>
>             > To: [hidden email]
>             <http:///user/SendEmail.jtp?type=node&node=1641912&i=4>;
>             [hidden email]
>             <http:///user/SendEmail.jtp?type=node&node=1641912&i=5>
>             > Subject: Re: [Gmod-ajax] data are not displayed even
>             though they were loaded (JBrowse)
>             >
>             > Can you do this:
>             >
>             > cd /var/www
>             > tar czf taro-tracks.tar.gz data/tracks
>             >
>             > That will create a file named taro-tracks.tar.gz, with
>             your generated
>             > data. Then can you email the file to me? That should
>             help me figure
>             > out what's going on.
>             >
>             > Mitch
>             >
>
>
>
>         ------------------------------------------------------------------------------
>         Beautiful is writing same markup. Internet Explorer 9 supports
>         standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
>         Spend less time writing and  rewriting code and more time creating great
>         experiences on the web. Be a part of the beta today.
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>
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>
>
>     ------------------------------------------------------------------------------
>
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>     great
>     experiences on the web. Be a part of the beta today.
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Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

[anja <fri...@ho...>]

yes

Date: Wed, 6 Oct 2010 04:56:55 -0700
From: ml-...@n3...
To: fri...@ho...
Subject: Re: data are not displayed even though they were loaded (JBrowse)





  
    
  
  
    The genome-2.css file is in /var/www?

    

    On 10/06/2010 04:51 AM, anja wrote:
    
      fixed everything but now I have a blank page...

      

      Anja

      

      Date: Wed, 6 Oct 2010 04:33:30 -0700

      From: [hidden email]

      To: [hidden email]

      Subject: Re: data are not displayed even though they were loaded
      (JBrowse)

      

      Hmmm, I know that we're very close, I tried out the data from your
      taro-tracks.tar.gz:

      

      http://jbrowse.org/test/anja/?loc=NC_010109.1:939..2254&tracks=DNA,nested_tandem_repeat

      

      I noticed two things when I was setting that up; one was that the
      CSS file that you sent was named genome-2.css.  The index.html
      file has to refer to the correct CSS file.  In the index.html
      file, there's a line like this:

      

          <link rel="stylesheet" type="text/css"
      href="genome.css"></link>

      

      I put your genome-2.css file in the same directory as the original
      genome.css, and changed that line in index.html to:

      

          <link rel="stylesheet" type="text/css"
      href="genome-2.css"></link>

      

      Also, in the CSS file you sent, there was a line like this:

      

          .minus-tall_orange, {

      

      which has an extra comma; it shouldn't have that comma at the end,
      like this:

      

          .minus-tall_orange {

      

      or, if the data is unstranded, it should look like this:

      

          .tall_orange {

      

      

      Also, some of the CSS classes were missing the "." at the
      beginning.

      

      Mitch

      

      

      

      On 10/06/2010 12:43 AM, Anja Friedrich wrote:
       Thank
        you very much for your time and help.

        I was afraid something like this will happen when I change it.
        But as I don't know whether they are stranded or not, I thought
        its better to mark it as unknown...

        I changed all the classes but it still won't display the motifs.
        Do I have to change it somewhere in addition?

        

        Anja

        Date: Tue, 5 Oct 2010 18:31:31 -0700

        From: [hidden email]

        To: [hidden email];
        [hidden email]

        Subject: Re: [Gmod-ajax] data are not displayed even though they
        were loaded (JBrowse)

        

        Okay, one of the GFF files that you sent earlier had strand
        information for the motifs.  I didn't notice that your later GFF
        files listed the motifs as being unstranded.

        

        That's why, in the CSS example I sent earlier, the CSS classes
        were all listed with separate "plus-" and "minus-" versions.

        

        If the motifs don't have strand information, then the CSS file
        should have CSS class names without those "plus-" and "minus-"
        prefixes.  For example, in the earlier example CSS file I sent,
        I had this:

        

        =====

        .plus-small_red,

        .plus-small_blue,

        .plus-small_purple,

        .plus-tall_blue,

        .plus-tall_purple,

        .minus-small_red,

        .minus-small_blue,

        .minus-small_purple,

        .minus-tall_blue,

        .minus-tall_purple {

            position: absolute;

            cursor: pointer;

            z-index: 10;

            min-width: 1px;

        }

        

        .plus-small_red, .minus-small_red {

            background-color: #EB2A2A; height: 6px; margin-top: -1px;

        }

        .plus-small_blue, .minus-small_blue {

            background-color: #46A1E0; height: 6px; margin-top: -1px;

        }

        .plus-small_purple, .minus-small_purple {

            background-color: #7322BF; height: 6px; margin-top: -1px;

        }

        .plus-tall_blue, .minus-tall_blue {

            background-color: #46A1E0; height: 10px; margin-top: -3px;

        }

        .plus-tall_purple, .minus-tall_purple {

            background-color: #7322BF; height: 10px; margin-top: -3px;

        }

        =====

        

        

        but if your motifs are unstranded, you could have this instead:

        

        

        =====

        .small_red,

        .small_blue,

        .small_purple,

        .tall_blue,

        .tall_purple {

            position: absolute;

            cursor: pointer;

            z-index: 10;

            min-width: 1px;

        }

        

        .small_red {

            background-color: #EB2A2A; height: 6px; margin-top: -1px;

        }

        .small_blue {

            background-color: #46A1E0; height: 6px; margin-top: -1px;

        }

        .small_purple {

            background-color: #7322BF; height: 6px; margin-top: -1px;

        }

        .tall_blue {

            background-color: #46A1E0; height: 10px; margin-top: -3px;

        }

        .tall_purple {

            background-color: #7322BF; height: 10px; margin-top: -3px;

        }

        =====

        

        

        Or, if your data has both stranded and unstranded features, you
        could include both stranded and unstranded versions of your CSS
        classes.

        

        Mitch

        

        On 10/05/2010 03:39 PM, Anja Friedrich wrote:
         done

          

          > Date: Tue, 5 Oct 2010 15:37:01 -0700

          > From: [hidden
            email]

          > To: [hidden
            email]; [hidden
            email]

          > Subject: Re: [Gmod-ajax] data are not displayed even
          though they were loaded (JBrowse)

          > 

          > Can you do this:

          > 

          > cd /var/www

          > tar czf taro-tracks.tar.gz data/tracks

          > 

          > That will create a file named taro-tracks.tar.gz, with
          your generated 

          > data. Then can you email the file to me? That should help
          me figure 

          > out what's going on.

          > 

          > Mitch

          > 

        
        

        
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      View this message in context: RE:
        data are not displayed even though they were loaded (JBrowse)

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        mailing list archive at Nabble.com.

      
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Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

[Mitch S. <mit...@be...>]

  The genome-2.css file is in /var/www?

On 10/06/2010 04:51 AM, anja wrote:
> fixed everything but now I have a blank page...
>
> Anja
>
> ------------------------------------------------------------------------
> Date: Wed, 6 Oct 2010 04:33:30 -0700
> From: [hidden email] </user/SendEmail.jtp?type=node&node=1641965&i=0>
> To: [hidden email] </user/SendEmail.jtp?type=node&node=1641965&i=1>
> Subject: Re: data are not displayed even though they were loaded (JBrowse)
>
> Hmmm, I know that we're very close, I tried out the data from your 
> taro-tracks.tar.gz:
>
> http://jbrowse.org/test/anja/?loc=NC_010109.1:939..2254&tracks=DNA,nested_tandem_repeat 
> <http://jbrowse.org/test/anja/?loc=NC_010109.1:939..2254&tracks=DNA,nested_tandem_repeat>
>
> I noticed two things when I was setting that up; one was that the CSS 
> file that you sent was named genome-2.css.  The index.html file has to 
> refer to the correct CSS file.  In the index.html file, there's a line 
> like this:
>
> <link rel="stylesheet" type="text/css" href="genome.css"></link>
>
> I put your genome-2.css file in the same directory as the original 
> genome.css, and changed that line in index.html to:
>
> <link rel="stylesheet" type="text/css" href="genome-2.css"></link>
>
> Also, in the CSS file you sent, there was a line like this:
>
>     .minus-tall_orange, {
>
> which has an extra comma; it shouldn't have that comma at the end, 
> like this:
>
>     .minus-tall_orange {
>
> or, if the data is unstranded, it should look like this:
>
>     .tall_orange {
>
>
> Also, some of the CSS classes were missing the "." at the beginning.
>
> Mitch
>
>
>
> On 10/06/2010 12:43 AM, Anja Friedrich wrote:
>
>     Thank you very much for your time and help.
>     I was afraid something like this will happen when I change it. But
>     as I don't know whether they are stranded or not, I thought its
>     better to mark it as unknown...
>     I changed all the classes but it still won't display the motifs.
>     Do I have to change it somewhere in addition?
>
>     Anja
>     ------------------------------------------------------------------------
>     Date: Tue, 5 Oct 2010 18:31:31 -0700
>     From: [hidden email]
>     <http:///user/SendEmail.jtp?type=node&node=1641912&i=0>
>     To: [hidden email]
>     <http:///user/SendEmail.jtp?type=node&node=1641912&i=1>; [hidden
>     email] <http:///user/SendEmail.jtp?type=node&node=1641912&i=2>
>     Subject: Re: [Gmod-ajax] data are not displayed even though they
>     were loaded (JBrowse)
>
>     Okay, one of the GFF files that you sent earlier had strand
>     information for the motifs.  I didn't notice that your later GFF
>     files listed the motifs as being unstranded.
>
>     That's why, in the CSS example I sent earlier, the CSS classes
>     were all listed with separate "plus-" and "minus-" versions.
>
>     If the motifs don't have strand information, then the CSS file
>     should have CSS class names without those "plus-" and "minus-"
>     prefixes.  For example, in the earlier example CSS file I sent, I
>     had this:
>
>     =====
>     .plus-small_red,
>     .plus-small_blue,
>     .plus-small_purple,
>     .plus-tall_blue,
>     .plus-tall_purple,
>     .minus-small_red,
>     .minus-small_blue,
>     .minus-small_purple,
>     .minus-tall_blue,
>     .minus-tall_purple {
>         position: absolute;
>         cursor: pointer;
>         z-index: 10;
>         min-width: 1px;
>     }
>
>     .plus-small_red, .minus-small_red {
>         background-color: #EB2A2A; height: 6px; margin-top: -1px;
>     }
>     .plus-small_blue, .minus-small_blue {
>         background-color: #46A1E0; height: 6px; margin-top: -1px;
>     }
>     .plus-small_purple, .minus-small_purple {
>         background-color: #7322BF; height: 6px; margin-top: -1px;
>     }
>     .plus-tall_blue, .minus-tall_blue {
>         background-color: #46A1E0; height: 10px; margin-top: -3px;
>     }
>     .plus-tall_purple, .minus-tall_purple {
>         background-color: #7322BF; height: 10px; margin-top: -3px;
>     }
>     =====
>
>
>     but if your motifs are unstranded, you could have this instead:
>
>
>     =====
>     .small_red,
>     .small_blue,
>     .small_purple,
>     .tall_blue,
>     .tall_purple {
>         position: absolute;
>         cursor: pointer;
>         z-index: 10;
>         min-width: 1px;
>     }
>
>     .small_red {
>         background-color: #EB2A2A; height: 6px; margin-top: -1px;
>     }
>     .small_blue {
>         background-color: #46A1E0; height: 6px; margin-top: -1px;
>     }
>     .small_purple {
>         background-color: #7322BF; height: 6px; margin-top: -1px;
>     }
>     .tall_blue {
>         background-color: #46A1E0; height: 10px; margin-top: -3px;
>     }
>     .tall_purple {
>         background-color: #7322BF; height: 10px; margin-top: -3px;
>     }
>     =====
>
>
>     Or, if your data has both stranded and unstranded features, you
>     could include both stranded and unstranded versions of your CSS
>     classes.
>
>     Mitch
>
>     On 10/05/2010 03:39 PM, Anja Friedrich wrote:
>
>         done
>
>         > Date: Tue, 5 Oct 2010 15:37:01 -0700
>         > From: [hidden email]
>         <http:///user/SendEmail.jtp?type=node&node=1641912&i=3>
>         > To: [hidden email]
>         <http:///user/SendEmail.jtp?type=node&node=1641912&i=4>;
>         [hidden email]
>         <http:///user/SendEmail.jtp?type=node&node=1641912&i=5>
>         > Subject: Re: [Gmod-ajax] data are not displayed even though
>         they were loaded (JBrowse)
>         >
>         > Can you do this:
>         >
>         > cd /var/www
>         > tar czf taro-tracks.tar.gz data/tracks
>         >
>         > That will create a file named taro-tracks.tar.gz, with your
>         generated
>         > data. Then can you email the file to me? That should help me
>         figure
>         > out what's going on.
>         >
>         > Mitch
>         >
>
>
>
>     ------------------------------------------------------------------------------
>     Beautiful is writing same markup. Internet Explorer 9 supports
>     standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
>     Spend less time writing and  rewriting code and more time creating great
>     experiences on the web. Be a part of the beta today.
>     http://p.sf.net/sfu/beautyoftheweb
>
>
>     _______________________________________________
>     Gmod-ajax mailing list
>     [hidden email]  <http:///user/SendEmail.jtp?type=node&node=1641912&i=6>
>     https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>
> ------------------------------------------------------------------------------ 
>
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
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>
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>
>
>
> ------------------------------------------------------------------------
> View this message in context: RE: data are not displayed even though 
> they were loaded (JBrowse) 
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> Sent from the JBrowse mailing list archive 
> <http://gmod.827538.n3.nabble.com/JBrowse-f815920.html> at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
>
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Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

[anja <fri...@ho...>]

fixed everything but now I have a blank page...

Anja

Date: Wed, 6 Oct 2010 04:33:30 -0700
From: ml-...@n3...
To: fri...@ho...
Subject: Re: data are not displayed even though they were loaded (JBrowse)





  
    
  
  
    Hmmm, I know that we're very close, I tried out the data from your
    taro-tracks.tar.gz:

    

http://jbrowse.org/test/anja/?loc=NC_010109.1:939..2254&tracks=DNA,nested_tandem_repeat

    

    I noticed two things when I was setting that up; one was that the
    CSS file that you sent was named genome-2.css.  The index.html file
    has to refer to the correct CSS file.  In the index.html file,
    there's a line like this:

    

        <link rel="stylesheet" type="text/css"
    href="genome.css"></link>

    

    I put your genome-2.css file in the same directory as the original
    genome.css, and changed that line in index.html to:

    

        <link rel="stylesheet" type="text/css"
    href="genome-2.css"></link>

    

    Also, in the CSS file you sent, there was a line like this:

    

        .minus-tall_orange, {

    

    which has an extra comma; it shouldn't have that comma at the end,
    like this:

    

        .minus-tall_orange {

    

    or, if the data is unstranded, it should look like this:

    

        .tall_orange {

    

    

    Also, some of the CSS classes were missing the "." at the beginning.

    

    Mitch

    

    

    

    On 10/06/2010 12:43 AM, Anja Friedrich wrote:
    
      
      Thank you very much for your time and help.

      I was afraid something like this will happen when I change it. But
      as I don't know whether they are stranded or not, I thought its
      better to mark it as unknown...

      I changed all the classes but it still won't display the motifs.
      Do I have to change it somewhere in addition?

      

      Anja

      Date: Tue, 5 Oct 2010 18:31:31 -0700

      From: [hidden email]

      To: [hidden email]; [hidden email]

      Subject: Re: [Gmod-ajax] data are not displayed even though they
      were loaded (JBrowse)

      

      
      
      Okay, one of the GFF files that you sent earlier had strand
      information for the motifs.  I didn't notice that your later GFF
      files listed the motifs as being unstranded.

      

      That's why, in the CSS example I sent earlier, the CSS classes
      were all listed with separate "plus-" and "minus-" versions.

      

      If the motifs don't have strand information, then the CSS file
      should have CSS class names without those "plus-" and "minus-"
      prefixes.  For example, in the earlier example CSS file I sent, I
      had this:

      

      =====

      .plus-small_red,

      .plus-small_blue,

      .plus-small_purple,

      .plus-tall_blue,

      .plus-tall_purple,

      .minus-small_red,

      .minus-small_blue,

      .minus-small_purple,

      .minus-tall_blue,

      .minus-tall_purple {

          position: absolute;

          cursor: pointer;

          z-index: 10;

          min-width: 1px;

      }

      

      .plus-small_red, .minus-small_red {

          background-color: #EB2A2A; height: 6px; margin-top: -1px;

      }

      .plus-small_blue, .minus-small_blue {

          background-color: #46A1E0; height: 6px; margin-top: -1px;

      }

      .plus-small_purple, .minus-small_purple {

          background-color: #7322BF; height: 6px; margin-top: -1px;

      }

      .plus-tall_blue, .minus-tall_blue {

          background-color: #46A1E0; height: 10px; margin-top: -3px;

      }

      .plus-tall_purple, .minus-tall_purple {

          background-color: #7322BF; height: 10px; margin-top: -3px;

      }

      =====

      

      

      but if your motifs are unstranded, you could have this instead:

      

      

      =====

      .small_red,

      .small_blue,

      .small_purple,

      .tall_blue,

      .tall_purple {

          position: absolute;

          cursor: pointer;

          z-index: 10;

          min-width: 1px;

      }

      

      .small_red {

          background-color: #EB2A2A; height: 6px; margin-top: -1px;

      }

      .small_blue {

          background-color: #46A1E0; height: 6px; margin-top: -1px;

      }

      .small_purple {

          background-color: #7322BF; height: 6px; margin-top: -1px;

      }

      .tall_blue {

          background-color: #46A1E0; height: 10px; margin-top: -3px;

      }

      .tall_purple {

          background-color: #7322BF; height: 10px; margin-top: -3px;

      }

      =====

      

      

      Or, if your data has both stranded and unstranded features, you
      could include both stranded and unstranded versions of your CSS
      classes.

      

      Mitch

      

      On 10/05/2010 03:39 PM, Anja Friedrich wrote:
      
         done

        

        > Date: Tue, 5 Oct 2010 15:37:01 -0700

        > From: [hidden email]

        > To: [hidden email];
        [hidden email]

        > Subject: Re: [Gmod-ajax] data are not displayed even though
        they were loaded (JBrowse)

        > 

        > Can you do this:

        > 

        > cd /var/www

        > tar czf taro-tracks.tar.gz data/tracks

        > 

        > That will create a file named taro-tracks.tar.gz, with your
        generated 

        > data. Then can you email the file to me? That should help
        me figure 

        > out what's going on.

        > 

        > Mitch

        > 

      
      

      
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Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

[anja <fri...@ho...>]

Oh great, thanks. I will fix it immediately.

Anja

Date: Wed, 6 Oct 2010 04:33:30 -0700
From: ml-...@n3...
To: fri...@ho...
Subject: Re: data are not displayed even though they were loaded (JBrowse)





  
    
  
  
    Hmmm, I know that we're very close, I tried out the data from your
    taro-tracks.tar.gz:

    

http://jbrowse.org/test/anja/?loc=NC_010109.1:939..2254&tracks=DNA,nested_tandem_repeat

    

    I noticed two things when I was setting that up; one was that the
    CSS file that you sent was named genome-2.css.  The index.html file
    has to refer to the correct CSS file.  In the index.html file,
    there's a line like this:

    

        <link rel="stylesheet" type="text/css"
    href="genome.css"></link>

    

    I put your genome-2.css file in the same directory as the original
    genome.css, and changed that line in index.html to:

    

        <link rel="stylesheet" type="text/css"
    href="genome-2.css"></link>

    

    Also, in the CSS file you sent, there was a line like this:

    

        .minus-tall_orange, {

    

    which has an extra comma; it shouldn't have that comma at the end,
    like this:

    

        .minus-tall_orange {

    

    or, if the data is unstranded, it should look like this:

    

        .tall_orange {

    

    

    Also, some of the CSS classes were missing the "." at the beginning.

    

    Mitch

    

    

    

    On 10/06/2010 12:43 AM, Anja Friedrich wrote:
    
      
      Thank you very much for your time and help.

      I was afraid something like this will happen when I change it. But
      as I don't know whether they are stranded or not, I thought its
      better to mark it as unknown...

      I changed all the classes but it still won't display the motifs.
      Do I have to change it somewhere in addition?

      

      Anja

      Date: Tue, 5 Oct 2010 18:31:31 -0700

      From: [hidden email]

      To: [hidden email]; [hidden email]

      Subject: Re: [Gmod-ajax] data are not displayed even though they
      were loaded (JBrowse)

      

      
      
      Okay, one of the GFF files that you sent earlier had strand
      information for the motifs.  I didn't notice that your later GFF
      files listed the motifs as being unstranded.

      

      That's why, in the CSS example I sent earlier, the CSS classes
      were all listed with separate "plus-" and "minus-" versions.

      

      If the motifs don't have strand information, then the CSS file
      should have CSS class names without those "plus-" and "minus-"
      prefixes.  For example, in the earlier example CSS file I sent, I
      had this:

      

      =====

      .plus-small_red,

      .plus-small_blue,

      .plus-small_purple,

      .plus-tall_blue,

      .plus-tall_purple,

      .minus-small_red,

      .minus-small_blue,

      .minus-small_purple,

      .minus-tall_blue,

      .minus-tall_purple {

          position: absolute;

          cursor: pointer;

          z-index: 10;

          min-width: 1px;

      }

      

      .plus-small_red, .minus-small_red {

          background-color: #EB2A2A; height: 6px; margin-top: -1px;

      }

      .plus-small_blue, .minus-small_blue {

          background-color: #46A1E0; height: 6px; margin-top: -1px;

      }

      .plus-small_purple, .minus-small_purple {

          background-color: #7322BF; height: 6px; margin-top: -1px;

      }

      .plus-tall_blue, .minus-tall_blue {

          background-color: #46A1E0; height: 10px; margin-top: -3px;

      }

      .plus-tall_purple, .minus-tall_purple {

          background-color: #7322BF; height: 10px; margin-top: -3px;

      }

      =====

      

      

      but if your motifs are unstranded, you could have this instead:

      

      

      =====

      .small_red,

      .small_blue,

      .small_purple,

      .tall_blue,

      .tall_purple {

          position: absolute;

          cursor: pointer;

          z-index: 10;

          min-width: 1px;

      }

      

      .small_red {

          background-color: #EB2A2A; height: 6px; margin-top: -1px;

      }

      .small_blue {

          background-color: #46A1E0; height: 6px; margin-top: -1px;

      }

      .small_purple {

          background-color: #7322BF; height: 6px; margin-top: -1px;

      }

      .tall_blue {

          background-color: #46A1E0; height: 10px; margin-top: -3px;

      }

      .tall_purple {

          background-color: #7322BF; height: 10px; margin-top: -3px;

      }

      =====

      

      

      Or, if your data has both stranded and unstranded features, you
      could include both stranded and unstranded versions of your CSS
      classes.

      

      Mitch

      

      On 10/05/2010 03:39 PM, Anja Friedrich wrote:
      
         done

        

        > Date: Tue, 5 Oct 2010 15:37:01 -0700

        > From: [hidden email]

        > To: [hidden email];
        [hidden email]

        > Subject: Re: [Gmod-ajax] data are not displayed even though
        they were loaded (JBrowse)

        > 

        > Can you do this:

        > 

        > cd /var/www

        > tar czf taro-tracks.tar.gz data/tracks

        > 

        > That will create a file named taro-tracks.tar.gz, with your
        generated 

        > data. Then can you email the file to me? That should help
        me figure 

        > out what's going on.

        > 

        > Mitch

        > 

      
      

      
------------------------------------------------------------------------------
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Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
      
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Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

[Mitch S. <mit...@be...>]

  Hmmm, I know that we're very close, I tried out the data from your 
taro-tracks.tar.gz:

http://jbrowse.org/test/anja/?loc=NC_010109.1:939..2254&tracks=DNA,nested_tandem_repeat

I noticed two things when I was setting that up; one was that the CSS 
file that you sent was named genome-2.css.  The index.html file has to 
refer to the correct CSS file.  In the index.html file, there's a line 
like this:

<link rel="stylesheet" type="text/css" href="genome.css"></link>

I put your genome-2.css file in the same directory as the original 
genome.css, and changed that line in index.html to:

<link rel="stylesheet" type="text/css" href="genome-2.css"></link>

Also, in the CSS file you sent, there was a line like this:

     .minus-tall_orange, {

which has an extra comma; it shouldn't have that comma at the end, like 
this:

     .minus-tall_orange {

or, if the data is unstranded, it should look like this:

     .tall_orange {


Also, some of the CSS classes were missing the "." at the beginning.

Mitch



On 10/06/2010 12:43 AM, Anja Friedrich wrote:
> Thank you very much for your time and help.
> I was afraid something like this will happen when I change it. But as 
> I don't know whether they are stranded or not, I thought its better to 
> mark it as unknown...
> I changed all the classes but it still won't display the motifs. Do I 
> have to change it somewhere in addition?
>
> Anja
> ------------------------------------------------------------------------
> Date: Tue, 5 Oct 2010 18:31:31 -0700
> From: mit...@be...
> To: fri...@ho...; gmo...@li...
> Subject: Re: [Gmod-ajax] data are not displayed even though they were 
> loaded (JBrowse)
>
> Okay, one of the GFF files that you sent earlier had strand 
> information for the motifs.  I didn't notice that your later GFF files 
> listed the motifs as being unstranded.
>
> That's why, in the CSS example I sent earlier, the CSS classes were 
> all listed with separate "plus-" and "minus-" versions.
>
> If the motifs don't have strand information, then the CSS file should 
> have CSS class names without those "plus-" and "minus-" prefixes.  For 
> example, in the earlier example CSS file I sent, I had this:
>
> =====
> .plus-small_red,
> .plus-small_blue,
> .plus-small_purple,
> .plus-tall_blue,
> .plus-tall_purple,
> .minus-small_red,
> .minus-small_blue,
> .minus-small_purple,
> .minus-tall_blue,
> .minus-tall_purple {
>     position: absolute;
>     cursor: pointer;
>     z-index: 10;
>     min-width: 1px;
> }
>
> .plus-small_red, .minus-small_red {
>     background-color: #EB2A2A; height: 6px; margin-top: -1px;
> }
> .plus-small_blue, .minus-small_blue {
>     background-color: #46A1E0; height: 6px; margin-top: -1px;
> }
> .plus-small_purple, .minus-small_purple {
>     background-color: #7322BF; height: 6px; margin-top: -1px;
> }
> .plus-tall_blue, .minus-tall_blue {
>     background-color: #46A1E0; height: 10px; margin-top: -3px;
> }
> .plus-tall_purple, .minus-tall_purple {
>     background-color: #7322BF; height: 10px; margin-top: -3px;
> }
> =====
>
>
> but if your motifs are unstranded, you could have this instead:
>
>
> =====
> .small_red,
> .small_blue,
> .small_purple,
> .tall_blue,
> .tall_purple {
>     position: absolute;
>     cursor: pointer;
>     z-index: 10;
>     min-width: 1px;
> }
>
> .small_red {
>     background-color: #EB2A2A; height: 6px; margin-top: -1px;
> }
> .small_blue {
>     background-color: #46A1E0; height: 6px; margin-top: -1px;
> }
> .small_purple {
>     background-color: #7322BF; height: 6px; margin-top: -1px;
> }
> .tall_blue {
>     background-color: #46A1E0; height: 10px; margin-top: -3px;
> }
> .tall_purple {
>     background-color: #7322BF; height: 10px; margin-top: -3px;
> }
> =====
>
>
> Or, if your data has both stranded and unstranded features, you could 
> include both stranded and unstranded versions of your CSS classes.
>
> Mitch
>
> On 10/05/2010 03:39 PM, Anja Friedrich wrote:
>
>     done
>
>     > Date: Tue, 5 Oct 2010 15:37:01 -0700
>     > From: mit...@be... <mailto:mit...@be...>
>     > To: gmo...@li...
>     <mailto:gmo...@li...>;
>     fri...@ho... <mailto:fri...@ho...>
>     > Subject: Re: [Gmod-ajax] data are not displayed even though they
>     were loaded (JBrowse)
>     >
>     > Can you do this:
>     >
>     > cd /var/www
>     > tar czf taro-tracks.tar.gz data/tracks
>     >
>     > That will create a file named taro-tracks.tar.gz, with your
>     generated
>     > data. Then can you email the file to me? That should help me figure
>     > out what's going on.
>     >
>     > Mitch
>     >
>
>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

[Anja F. <fri...@ho...>]

Thank you very much for your time and help.
I was afraid something like this will happen when I change it. But as I don't know whether they are stranded or not, I thought its better to mark it as unknown...
I changed all the classes but it still won't display the motifs. Do I have to change it somewhere in addition?

Anja
Date: Tue, 5 Oct 2010 18:31:31 -0700
From: mit...@be...
To: fri...@ho...; gmo...@li...
Subject: Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)



  


    
  
  
    Okay, one of the GFF files that you sent earlier had strand
    information for the motifs.  I didn't notice that your later GFF
    files listed the motifs as being unstranded.

    

    That's why, in the CSS example I sent earlier, the CSS classes were
    all listed with separate "plus-" and "minus-" versions.

    

    If the motifs don't have strand information, then the CSS file
    should have CSS class names without those "plus-" and "minus-"
    prefixes.  For example, in the earlier example CSS file I sent, I
    had this:

    

    =====

    .plus-small_red,

    .plus-small_blue,

    .plus-small_purple,

    .plus-tall_blue,

    .plus-tall_purple,

    .minus-small_red,

    .minus-small_blue,

    .minus-small_purple,

    .minus-tall_blue,

    .minus-tall_purple {

        position: absolute;

        cursor: pointer;

        z-index: 10;

        min-width: 1px;

    }

    

    .plus-small_red, .minus-small_red {

        background-color: #EB2A2A; height: 6px; margin-top: -1px;

    }

    .plus-small_blue, .minus-small_blue {

        background-color: #46A1E0; height: 6px; margin-top: -1px;

    }

    .plus-small_purple, .minus-small_purple {

        background-color: #7322BF; height: 6px; margin-top: -1px;

    }

    .plus-tall_blue, .minus-tall_blue {

        background-color: #46A1E0; height: 10px; margin-top: -3px;

    }

    .plus-tall_purple, .minus-tall_purple {

        background-color: #7322BF; height: 10px; margin-top: -3px;

    }

    =====

    

    

    but if your motifs are unstranded, you could have this instead:

    

    

    =====

    .small_red,

    .small_blue,

    .small_purple,

    .tall_blue,

    .tall_purple {

        position: absolute;

        cursor: pointer;

        z-index: 10;

        min-width: 1px;

    }

    

    .small_red {

        background-color: #EB2A2A; height: 6px; margin-top: -1px;

    }

    .small_blue {

        background-color: #46A1E0; height: 6px; margin-top: -1px;

    }

    .small_purple {

        background-color: #7322BF; height: 6px; margin-top: -1px;

    }

    .tall_blue {

        background-color: #46A1E0; height: 10px; margin-top: -3px;

    }

    .tall_purple {

        background-color: #7322BF; height: 10px; margin-top: -3px;

    }

    =====

    

    

    Or, if your data has both stranded and unstranded features, you
    could include both stranded and unstranded versions of your CSS
    classes.

    

    Mitch

    

    On 10/05/2010 03:39 PM, Anja Friedrich wrote:
    
      
      done

      

      > Date: Tue, 5 Oct 2010 15:37:01 -0700

      > From: mit...@be...

      > To: gmo...@li...;
      fri...@ho...

      > Subject: Re: [Gmod-ajax] data are not displayed even though
      they were loaded (JBrowse)

      > 

      > Can you do this:

      > 

      > cd /var/www

      > tar czf taro-tracks.tar.gz data/tracks

      > 

      > That will create a file named taro-tracks.tar.gz, with your
      generated 

      > data. Then can you email the file to me? That should help me
      figure 

      > out what's going on.

      > 

      > Mitch

      >