gmod-ajax — JBrowse list

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

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

  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
> >

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

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

  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
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> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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

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

  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

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

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

I zoomed in as much as possible (and it is far enough when I look at the "ruler") but I still can't see anything. Only the DNA track was added. I hope the config file and genome.css are right... but I attached them

Date: Tue, 5 Oct 2010 14:55:40 -0700
From: ml-...@n3...
To: fri...@ho...
Subject: Re: data are not displayed even though they were loaded (JBrowse)



  Do the motifs show up if you zoom in?


The motifs should show up, assuming that:


1. you have "subfeatures": true and "subfeature_classes" in your config 

file, like this:


       "subfeatures": true,

       "subfeature_classes": {

         "motif1_small_a": "small_red",

         "motif1_small_b": "small_blue",

         "motif1_small_c": "small_purple",

         "motif1_tall_a": "tall_blue",

         "motif1_tall_b": "tall_purple"

       }


and 2. /var/www/genome.css has a listing for all of the values in the 

"subfeature_classes" setting.


If have both of those things, then my best guess for what's going on is 

this: by default, subfeatures like your motifs are only shown once you 

zoom in beyond a certain level.


The threshold where they show up is controlled by the "subfeatureScale" 

setting in the "clientConfig" part of the config file, so you can add 

something like this:


       "clientConfig": {

           "subfeatureScale": 40

       },


The default is 80, and if you want the subfeatures to still show up when 

you're more zoomed out, set it lower.


The actual units for the "subfeatureScale" setting are pixels/feature.  

That value is multiplied by the average feature density in features/base 

units (i.e., the number of features in the track / the refseq length) to 

get the scale threshold in pixels per base.  For example, if the 

subfeatureScale is 2, and a track has 100 features, then subfeatures 

will be shown if you're zoomed in far enough that the entire refseq 

would be at least 200 pixels wide.


Hope this helps,

Mitch


On 10/05/2010 02:24 PM, anja wrote:

> Hi Mitch,

>

> when I visit http://localhost/ then I see the surface of JBrowse and 

> the track as a grey line, so no motifs at all... more then before I guess



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

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html, body {
    height: 98%;
}

.nav {
    vertical-align: middle;
    z-index: 10;
}

input.icon {
    display: -moz-inline-stack;
    display: inline-block;
    zoom: 1;
    *display: inline;
}

div.container {
    position: absolute;
    z-index: 0;
}

div.dragWindow {
    position:absolute;
    overflow: hidden;
    z-index: 1;
    cursor: url("openhand.cur");
}

div.locationTrap {
    position: absolute;
    background-color: #BDD7FF;
    border-color: white white #BDD7FF white;
    border-style: solid;
    width: 0px;
    height: 0px;
    line-height: 0px;
    z-index: -10;
}

div.locationThumb {
    position: absolute;
    top: 0px;
    /* if you change this border from 2px, change GenomeView.showTrap */
    border: 2px solid red;
    margin: 0px -2px 0px -2px;
    cursor: url("openhand.cur");
}

div.locationThumb.dojoMoveItem {
    cursor: url("closedhand.cur");
}

div.overview {
    width: 100%;
    border-style: solid;
    border-width: 5px 0px 5px 0px;
    border-color: #aaa;
    color:#aaa;
    font-family: sans-serif;
    text-align: center;
    z-index: -5;
}

div.block {
    position: absolute;
    overflow: visible;
    top: 0px;
    height: 100%;
}

div.track {
    position: absolute;
    left: 0px;
    width: 100%;
    z-index: 5;
}

.track.dojoDndItemOver {
    cursor: inherit;
}

.track.dojoDndItemBefore {
    border-top: 3px solid #999;
    margin-top: -3px;
}

.track.dojoDndItemAfter {
    border-bottom: 3px solid #999;
    margin-bottom: -3px;
}

div#static_track {
    top: 0px;
    position: absolute;
    background-color: #f0f0f0;
    z-index: 20;
}

div.gridline {
    position: absolute;
    top: 0px;
    height: 100%;
    border-style: none none none solid;
    border-width: 1px;
    border-color: #ddd;
}

div.pos-label {
    position: absolute;
    left: 0px;
    background-color: #ddd;
    z-index: 100;
    padding: 4px;
    font-family: sans-serif;
}

div.overview-pos {
    position: absolute;
    left: 0px;
    color: black;
    padding-left: 4px;
    font-family: sans-serif;
    border-style: solid;
    border-color: black;
    border-width: 0px 0px 0px 1px;
}

div.blank-block {
    font: sans-serif;
    position: absolute;
    overflow: visible;
    top: 0px;
    height: 100%;
    background-color: #eee;
    z-index: 19;
}

div.sequence {
    position: absolute;
    left: 0px;
    font-family: monospace;
    letter-spacing: 2px;
    padding-left: 2px;
}

/*
div.minus-feature:before {
    content: attr(fName);
    display: block;
}

div.plus-feature:before {
    content: attr(fName);
    display: inline;
}
*/

div.track-label {
    font-family: sans-serif;
    z-index: 20;
    background-color: #BDD7FF;
    border: 2px #2b434c solid;
    color: #2b434c;
    padding: 5px;
    cursor: pointer;
}

div.tracklist-label {
    font-family: sans-serif;
    z-index: 20;
    background-color: #BDD7FF;
    border: 2px #2b434c solid;
    color: #2b434c;
    cursor: pointer;
    padding: 3px;
}

/* commented for now, multi-select too confusing?
.tracklist-container.dojoDndItemSelected {
    background: #ddf;
}

.tracklist-container.dojoDndItemAnchor {
    background: #ddf;
}
*/

div.tracklist-container {
    padding: 5px;
    margin-top: -3px;
    margin-bottom: -3px;
}

.tracklist-container.dojoDndItemBefore {
    border-top: 3px solid #999;
    padding-top: 2px;
}

.tracklist-container.dojoDndItemAfter {
    border-bottom: 3px solid #999;
    padding-bottom: 2px;
}

.feature-label {
    position: absolute;
    font-family: monospace;
    border: 0px;
    margin: -2px 0px 0px 0px;
    /* padding: 0px 0px 2px 0px; for more space below labels */
    padding: 0px 0px 0px 0px;
    /* font-size: 80%; */
    white-space: nowrap;
    background-color: #eee;
    z-index: 10;
    cursor: pointer;
}

.basic,
.plus-basic,
.minus-basic {
    position: absolute;
    cursor: pointer;
    z-index: 10;
    min-width: 1px;
}

div.basic-hist {
    position: absolute;
    z-index: 10;
}

.plus-feature,
.minus-feature {
    position:absolute;
    height: 8px;
    background-repeat: repeat-x;
    cursor: pointer;
    min-width: 1px;
    z-index: 10;
}

.plus-feature { background-image: url('img/plus-chevron3.png'); }

.minus-feature { background-image: url('img/minus-chevron3.png'); }

div.feature-hist {
    position: absolute;
    background-color: blue;
    border-color: lightblue;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.plus-feature2,
.minus-feature2 {
    position:absolute;
    height: 15px;
    background-repeat: repeat-x;
    cursor: pointer;
    min-width: 1px;
    z-index: 10;
}

.plus-feature2 { background-image: url('img/plus-herringbone16.png'); }

.minus-feature2 { background-image: url('img/minus-herringbone16.png'); }

div.feature2-hist {
    position: absolute;
    background-color: #9f9;
    border-color: #ada;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.plus-feature3,
.minus-feature3 {
    position:absolute;
    height: 8px;
    background-repeat: repeat-x;
    cursor: pointer;
    min-width: 1px;
    z-index: 10;
}

.plus-feature3 { background-image: url('img/plus-chevron.png'); }

.minus-feature3 { background-image: url('img/minus-chevron.png'); }

div.feature3-hist {
    position: absolute;
    background-color: yellow;
    border-color: black;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.plus-feature4,
.minus-feature4 {
    position:absolute;
    height: 12px;
    background-repeat: repeat-x;
    cursor: pointer;
    min-width: 1px;
    z-index: 10;
}

.plus-feature4 { background-image: url('img/plus-pacman.png'); }

.minus-feature4 { background-image: url('img/minus-pacman.png'); }

div.feature4-hist {
    position: absolute;
    background-color: yellow;
    border-color: black;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.plus-feature5,
.minus-feature5 {
    position:absolute;
    height: 8px;
    background-repeat: repeat-x;
    cursor: pointer;
    min-width: 1px;
    z-index: 10;
}

.plus-feature5 { background-image: url('img/plus-chevron2.png'); }

.minus-feature5 { background-image: url('img/minus-chevron2.png'); }

div.feature5-hist {
    position: absolute;
    background-color: blue;
    border-color: lightblue;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

div.exon-hist {
    position: absolute;
    background-color: #4B76E8;
    border-style: solid;
    border-color: #00f;
    border-width: 1px;
    z-index: 10;
}

.plus-exon,
.minus-exon {
    position: absolute;
    height: 5px;
    background-color: #4B76E8;
    border-style: solid;
    border-color: #00f;
    border-width: 1px;
    cursor: pointer;
    z-index: 10;
}

div.est-hist {
    position: absolute;
    background-color: #ED9185;
    border-style: solid;
    border-color: #c33;
    border-width: 1px;
    z-index: 10;
}

.plus-est,
.minus-est {
    position: absolute;
    height: 5px;
    background-color: #ED9185;
    border-style: solid;
    border-color: #c33;
    border-width: 1px;
    cursor: pointer;
    z-index: 10;
}

.plus-dblhelix,
.minus-dblhelix {
    position:absolute;
    height: 11px;
    background-image: url('img/dblhelix-red.png');
    background-repeat: repeat-x;
    min-width: 1px;
    cursor: pointer;
    z-index: 10;
}

div.dblhelix-hist {
    position: absolute;
    background-color: #fcc;
    border-color: #daa;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.plus-helix,
.minus-helix {
    position:absolute;
    height: 12px;
    background-image: url('img/helix3-green.png');
    background-repeat: repeat-x;
    min-width: 1px;
    cursor: pointer;
    z-index: 10;
}

div.helix-hist {
    position: absolute;
    background-color: #cfc;
    border-color: #ada;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.loops {
    position:absolute;
    height: 13px;
    background-image: url('img/loops.png');
    background-repeat: repeat-x;
    cursor: pointer;
}

.plus-cds0, .plus-cds1, .plus-cds2,
.minus-cds0, .minus-cds1, .minus-cds2 {
    position:absolute;
    height: 13px;
    background-repeat: repeat-x;
    cursor: pointer;
    min-width: 1px;
}

.plus-cds0 { background-image: url('img/plus-cds0.png'); }
.plus-cds1 { background-image: url('img/plus-cds1.png'); }
.plus-cds2 { background-image: url('img/plus-cds2.png'); }
.minus-cds0 { background-image: url('img/minus-cds0.png'); }
.minus-cds1 { background-image: url('img/minus-cds1.png'); }
.minus-cds2 { background-image: url('img/minus-cds2.png'); }

div.cds-hist {
    position: absolute;
    background-color: #fcc;
    border-color: #daa;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.topbracket {
    position:absolute;
    height: 8px;
    border-style: solid solid none solid;
/*    border-width: 2px 2px 0px 2px; */
    border-width: 2px;
    border-color: orange;
/*    margin-top: 2px */
    cursor: pointer;
}

.bottombracket {
    position:absolute;
    height: 8px;
    border-style: none solid solid solid;
    border-width: 2px;
    border-color: green;
    cursor: pointer;
}

.hourglass {
    position:absolute;
    height: 0px;
    border-style: solid;
    border-width: 6px 3px 6px 3px;
    cursor: pointer;
}

.plus-triangle {
    position:absolute;
    height: 0px;
    border-style: solid;
    border-width: 6px 3px 0px 3px;
    cursor: pointer;
}

.minus-triangle {
    position:absolute;
    height: 0px;
    border-style: solid;
    border-width: 0px 3px 6px 3px;
    cursor: pointer;
}

.triangle {
    position:absolute;
    height: 0px;
    border-style: solid;
    border-width: 6px 0px 0px 0px;
    cursor: pointer;
}

.hgred {
    border-color: #f99 white #f99 white;
}
div.hgred-hist {
    position: absolute;
    background-color: #daa;
    border-color: #d44;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.hgblue {
    border-color: #99f white #99f white;
}
div.hgblue-hist {
    position: absolute;
    background-color: #aad;
    border-color: #99f;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.ibeam {
    position:absolute;
    height: 2px;
    background-color: blue;
    border-style: solid;
    border-width: 8px 4px 8px 4px;
    border-color: white blue white blue;
    cursor: pointer;
}

div.transcript-hist {
    position: absolute;
    background-color: #ddd;
    border-color: #FF9185;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.transcript,
.plus-transcript,
.minus-transcript {
    position: absolute;
    height: 4px;
    margin-top: 4px;
    margin-bottom: 4px;
    background-color: #999;
    z-index: 6;
    min-width: 1px;
    cursor: pointer;
}

.plus-transcript-arrowhead {
    position: absolute;
/*  border stuff seems slow
    height: 0px;
    width: 0px;
    margin-top: -4px;
    border-style: solid;
    border-color: white white white #999;
    border-width: 6px 0px 6px 10px; */
    margin-top: -4px;
    width: 12px;
    height: 12px;
    background-image: url('img/plus-transcript-head.png');
    background-repeat: no-repeat;
}

.minus-transcript-arrowhead {
    position: absolute;
/*  border stuff seems slow
    height: 0px;
    width: 0px;
    margin-top: -4px;
    border-style: solid;
    border-color: white #999 white white;
    border-width: 6px 10px 6px 0px; */
    margin-top: -4px;
    width: 12px;
    height: 12px;
    background-image: url('img/minus-transcript-head.png');
    background-repeat: no-repeat;
}

.plus-transcript-CDS,
.minus-transcript-CDS {
    position: absolute;
    height: 12px;
    margin-top: -4px;
    background-image: url('img/cds.png');
    background-repeat: repeat-x;
/*  border-width: 2px 0px 3px 0px;
    border-style: solid;
    border-color: white;
    background-color: #FF9185;
    border-style: solid;
    border-color: #00f;
    border-width: 1px;*/
    cursor: pointer;
    z-index: 10;
    min-width: 1px;
}

.plus-transcript-exon,
.minus-transcript-exon,
.plus-transcript-UTR, 
.minus-transcript-UTR,
.plus-transcript-five_prime_UTR,
.minus-transcript-five_prime_UTR,
.plus-transcript-three_prime_UTR,
.minus-transcript-three_prime_UTR {
    position: absolute;
    height: 4px;
    margin-top: -2px;
    background-color: #B66;
    border-style: solid;
    border-color: #D88;
    border-width: 2px 0px 2px 0px;
    z-index: 8;
    min-width: 1px;
    cursor: pointer;
}

.generic_parent,
.plus-generic_parent,
.minus-generic_parent {
    position: absolute;
    height: 4px;
    margin-top: 2px;
    margin-bottom: 2px;
    background-color: #AAA;
    z-index: 6;
    min-width: 1px;
    cursor: pointer;
}

div.generic_parent-hist {
    position: absolute;
    background-color: #ddd;
    border-color: #555;
    border-style: solid;
    border-width: 1px;
    z-index: 10;
}

.match_part,
.plus-match_part,
.minus-match_part {
    position: absolute;
    height: 4px;
    margin-top: -2px;
    background-color: #66B;
    border-style: solid;
    border-color: #88D;
    border-width: 2px 0px 2px 0px;
    z-index: 8;
    min-width: 1px;
    cursor: pointer;
}

.generic_part_a,
.plus-generic_part_a,
.minus-generic_part_a {
    position: absolute;
    height: 4px;
    margin-top: -2px;
    background-color: #6B6;
    border-style: solid;
    border-color: #8D8;
    border-width: 2px 0px 2px 0px;
    z-index: 8;
    min-width: 1px;
    cursor: pointer;
}

.plus-small_red,
.plus-small_blue,
.plus-small_purple,
.plus-small_green,
.plus-small_orange,
.plus-small_black,
.plus-small_pink,
.plus-small_brown,
.plus-small_yellow,
.plus-small_violet,
.plus-small_aqua,
.plus-small_fuchsia,
.plus-tall_blue,
.plus-tall_purple,
.plus-tall_red,
.plus-tall_yellow,
.plus-tall_brown,
.plus-tall_orange,
.minus-small_red,
.minus-small_blue,
.minus-small_purple,
.minus-small_green,
.minus-small_orange,
.minus-small_black,
.minus-small_pink,
.minus-small_brown,
.minus-small_yellow,
.minus-small_violet,
.minus-small_aqua,
.minus-small_fuchsia,
.minus-tall_blue,
.minus-tall_purple
.minus-tall_red,
.minus-tall_yellow,
.minus-tall_brown,
.minus-tall_orange, {
    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-small_purple, .minus-small_green {
    background-color: #008000; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_orange {
    background-color: #FFA500; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_black {
    background-color: #000000; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_pink {
    background-color: #FFC0CB; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_brown {
    background-color: #A52A2A; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_yellow {
    background-color: #FFFF00; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_violet {
    background-color: #C71585; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_aqua {
    background-color: #00FFFF; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_fuchsia {
    background-color: #FF00FF; 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;
}
plus-tall_blue, .minus-tall_yellow {
    background-color: #FFFF00; height: 10px; margin-top: -3px;
}
plus-tall_blue, .minus-tall_brown {
    background-color: #A52A2A; height: 10px; margin-top: -3px;
}
plus-tall_blue, .minus-tall_orange {
    background-color: #FFA500; height: 10px; margin-top: -3px;
}

 

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

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

  Do the motifs show up if you zoom in?

The motifs should show up, assuming that:

1. you have "subfeatures": true and "subfeature_classes" in your config 
file, like this:

       "subfeatures": true,
       "subfeature_classes": {
         "motif1_small_a": "small_red",
         "motif1_small_b": "small_blue",
         "motif1_small_c": "small_purple",
         "motif1_tall_a": "tall_blue",
         "motif1_tall_b": "tall_purple"
       }

and 2. /var/www/genome.css has a listing for all of the values in the 
"subfeature_classes" setting.

If have both of those things, then my best guess for what's going on is 
this: by default, subfeatures like your motifs are only shown once you 
zoom in beyond a certain level.

The threshold where they show up is controlled by the "subfeatureScale" 
setting in the "clientConfig" part of the config file, so you can add 
something like this:

       "clientConfig": {
           "subfeatureScale": 40
       },

The default is 80, and if you want the subfeatures to still show up when 
you're more zoomed out, set it lower.

The actual units for the "subfeatureScale" setting are pixels/feature.  
That value is multiplied by the average feature density in features/base 
units (i.e., the number of features in the track / the refseq length) to 
get the scale threshold in pixels per base.  For example, if the 
subfeatureScale is 2, and a track has 100 features, then subfeatures 
will be shown if you're zoomed in far enough that the entire refseq 
would be at least 200 pixels wide.

Hope this helps,
Mitch

On 10/05/2010 02:24 PM, anja wrote:
> Hi Mitch,
>
> when I visit http://localhost/ then I see the surface of JBrowse and 
> the track as a grey line, so no motifs at all... more then before I guess

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

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

Hi Mitch, 

when I visit http://localhost/ then I see the surface of JBrowse and the track as a grey line, so no motifs at all... more then before I guess

Anja

Date: Tue, 5 Oct 2010 14:15:32 -0700
From: ml-...@n3...
To: fri...@ho...
Subject: Re: data are not displayed even though they were loaded (JBrowse)





  
    
    E-Mail-Text
  
  
    I'm not totally sure what's going on for you, but here's my best
    guess:

    

    Usually, web servers are set up so that one particular path (e.g.,
    /var/www) becomes the "root" of the space on the web server.  So,
    for example, if you put a file named "foo.html" into /var/www, so
    that the full path is /var/www/foo.html, then it'll show up in the
    web server as /foo.html.  So if you're accessing the web server on
    your laptop, you can see that HTML page by going to
    http://localhost/foo.html.

    

    Different linux distributions put the "root" of the web server space
    in different places; in ubuntu (and distributions based on ubuntu,
    like Mint), it's /var/www.  In distributions derived from Red Hat,
    it's /var/www/html.

    

    In your case, it looks like it's /var/www, so if you want to see
    what's in /var/www, you can visit http://localhost/ in your web
    browser.  If you look there, do you see your data?

    

    Mitch

    

    On 10/04/2010 11:52 AM, Anja Friedrich wrote:
    
      
      Hi all, 

      

      I was using SeqFeature Store to load data and display them in
      JBrowse. But I an't see anything. They are not displayed at all
      like they don't exist... Do I activate it wrong? I was looking
      under http://localhost/jbrowse/

      I used this commandos and it looks as if the data were loaded...
      

        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

      anou@anou-laptop:/var/www$ bin/generate-names.pl 

      

      Anja

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

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

  I'm not totally sure what's going on for you, but here's my best guess:

Usually, web servers are set up so that one particular path (e.g., 
/var/www) becomes the "root" of the space on the web server.  So, for 
example, if you put a file named "foo.html" into /var/www, so that the 
full path is /var/www/foo.html, then it'll show up in the web server as 
/foo.html.  So if you're accessing the web server on your laptop, you 
can see that HTML page by going to http://localhost/foo.html.

Different linux distributions put the "root" of the web server space in 
different places; in ubuntu (and distributions based on ubuntu, like 
Mint), it's /var/www.  In distributions derived from Red Hat, it's 
/var/www/html.

In your case, it looks like it's /var/www, so if you want to see what's 
in /var/www, you can visit http://localhost/ in your web browser.  If 
you look there, do you see your data?

Mitch

On 10/04/2010 11:52 AM, Anja Friedrich wrote:
> Hi all,
>
> I was using SeqFeature Store to load data and display them in JBrowse. 
> But I an't see anything. They are not displayed at all like they don't 
> exist... Do I activate it wrong? I was looking under 
> http://localhost/jbrowse/
> I used this commandos and it looks as if the data were loaded...
>
> anou@anou-laptop:/var/www$ bp_seqfeature_load.pl 
> <http://bp_seqfeature_load.pl/?by-user=t> --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 
> <http://prepare-refseqs.pl/?by-user=t> --conf taro.json --refs NC_010109.1
> anou@anou-laptop:/var/www$ bin/biodb-to-json.pl 
> <http://biodb-to-json.pl/?by-user=t> --conf taro.json
>
> working on refseq NC_010109.1
> working on track nested_tandem_repeat
> got 1 features for nested_tandem_repeat
> anou@anou-laptop:/var/www$ bin/generate-names.pl
>
> Anja
>
>
> ------------------------------------------------------------------------------
> Virtualization is moving to the mainstream and overtaking non-virtualized
> environment for deploying applications. Does it make network security
> easier or more difficult to achieve? Read this whitepaper to separate the
> two and get a better understanding.
> http://p.sf.net/sfu/hp-phase2-d2d
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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

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

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

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

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

Hi all, 

I was using SeqFeature Store to load data and display them in JBrowse. But I an't see anything. They are not displayed at all like they don't exist... Do I activate it wrong? I was looking under  http://localhost/jbrowse/
I used this commandos and it looks as if the data were loaded...
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
anou@anou-laptop:/var/www$ bin/generate-names.pl 

Anja
 		 	   		  

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

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

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

>

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

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> and start using them to simplify application deployment and

> accelerate your shift to cloud computing.

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>

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

Ontario Institute for Cancer Research


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

[Scott C. <sc...@sc...>]

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 <fri...@ho...> 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]<http://user/SendEmail.jtp?type=node&node=1615989&i=0>
> To: [hidden email] <http://user/SendEmail.jtp?type=node&node=1615989&i=1>
> 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]<http:///user/SendEmail.jtp?type=node&node=1615837&i=0>
> > 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]<http:///user/SendEmail.jtp?type=node&node=1615837&i=1>
> To: [hidden email] <http:///user/SendEmail.jtp?type=node&node=1615837&i=2>
> CC: [hidden email] <http:///user/SendEmail.jtp?type=node&node=1615837&i=3>
>
>
> Hi Anja,
>
> The argument for the prepare-refseqs.pl<http://prepare-refseqs.pl?by-user=t&by-user=t>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]<http:///user/SendEmail.jtp?type=node&node=1615837&i=4>
> > wrote:
>
> Hi Scott,
>
> I attached it
>
> Anja
>
> ------------------------------
> Date: Fri, 1 Oct 2010 06:01:51 -0700
> From: [hidden email]<http://user/SendEmail.jtp?type=node&node=1614664&i=0>
> To: [hidden email] <http://user/SendEmail.jtp?type=node&node=1614664&i=1>
> 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] <http:///user/SendEmail.jtp?type=node&node=1614559&i=0>>
> wrote:
>
> > Hi all,
> >
> > I finally managed to load the data and to run bin/prepare-refseqs.pl<http://prepare-refseqs.pl?by-user=t&by-user=t>
> >
> > anou@anou-laptop:/var/www$ bp_seqfeature_load.pl<http://bp_seqfeature_load.pl?by-user=t&by-user=t>--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<http://prepare-refseqs.pl?by-user=t&by-user=t>--conf taro.json --refs
> > NC_010109.1
> > anou@anou-laptop:/var/www$ bin/biodb-to-json.pl<http://biodb-to-json.pl?by-user=t&by-user=t>--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] <http:///user/SendEmail.jtp?type=node&node=1614559&i=1>
> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >
> >
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)  <http://gmod.org/%29%C2%A0>
>          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
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email] <http:///user/SendEmail.jtp?type=node&node=1614559&i=2>
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> ------------------------------
>  View message @
> http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1614559.html<http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1614559.html?by-user=t&by-user=t&by-user=t>
> To start a new topic under GMOD, email [hidden email]<http://user/SendEmail.jtp?type=node&node=1614664&i=2>
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>
>
>
>
> *taro.gff* (11K) Download Attachment<http://attachment/1614664/0/taro.gff>
>
> ------------------------------
> View this message in context: RE: 0 features found/no display of data<http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1614664.html?by-user=t&by-user=t>
> Sent from the JBrowse mailing list archive<http://gmod.827538.n3.nabble.com/JBrowse-f815920.html?by-user=t&by-user=t>at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> 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] <http:///user/SendEmail.jtp?type=node&node=1615837&i=5>
> 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
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email] <http:///user/SendEmail.jtp?type=node&node=1615837&i=6>
> 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
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email] <http:///user/SendEmail.jtp?type=node&node=1615837&i=7>
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> ------------------------------
>  View message @
> http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1615837.html<http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1615837.html?by-user=t>
> To start a new topic under GMOD, email [hidden email]<http://user/SendEmail.jtp?type=node&node=1615989&i=2>
> To unsubscribe from GMOD, click here<http://gmod.827538.n3.nabble.com/template/TplServlet.jtp?tpl=unsubscribe_by_code&node=827538&code=ZnJpZWRyaWNoLmFuamFAaG90bWFpbC5kZXw4Mjc1Mzh8MzI2MTcxMzA3&by-user=t>.
>
>
>
> ------------------------------
> View this message in context: RE: 0 features found/no display of data<http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1615989.html>
> Sent from the JBrowse mailing list archive<http://gmod.827538.n3.nabble.com/JBrowse-f815920.html>at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> 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
>
>


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

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

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

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: ml-...@n3...
To: fri...@ho...
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

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[hidden email]

https://lists.sourceforge.net/lists/listinfo/gmod-ajax






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To start a new topic under GMOD, email [hidden email]

To unsubscribe from GMOD, click here.


 		 	   		  

 
 taro.gff (11K) Download Attachment


View this message in context: RE: 0 features found/no display of data

Sent from the JBrowse mailing list archive at Nabble.com.


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

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and start using them to simplify application deployment and

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



Ontario Institute for Cancer Research
 		 	   		  

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

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and start using them to simplify application deployment and

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-- 
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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

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View this message in context: http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1615989.html
Sent from the JBrowse mailing list archive at Nabble.com.

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

[Scott C. <sc...@sc...>]

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
<fri...@ho...>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: sc...@sc...
> To: fri...@ho...
> CC: gmo...@li...
>
>
> 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 <fri...@ho...> wrote:
>
> Hi Scott,
>
> I attached it
>
> Anja
>
> ------------------------------
> Date: Fri, 1 Oct 2010 06:01:51 -0700
> From: [hidden email]<http://user/SendEmail.jtp?type=node&node=1614664&i=0>
> To: [hidden email] <http://user/SendEmail.jtp?type=node&node=1614664&i=1>
> 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] <http:///user/SendEmail.jtp?type=node&node=1614559&i=0>>
> 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] <http:///user/SendEmail.jtp?type=node&node=1614559&i=1>
> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >
> >
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)  <http://gmod.org/%29%C2%A0>
>          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
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email] <http:///user/SendEmail.jtp?type=node&node=1614559&i=2>
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> ------------------------------
>  View message @
> http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1614559.html<http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1614559.html?by-user=t>
> To start a new topic under GMOD, email [hidden email]<http://user/SendEmail.jtp?type=node&node=1614664&i=2>
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>
>
>
>
> *taro.gff* (11K) Download Attachment<http://attachment/1614664/0/taro.gff>
>
> ------------------------------
> View this message in context: RE: 0 features found/no display of data<http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1614664.html>
> Sent from the JBrowse mailing list archive<http://gmod.827538.n3.nabble.com/JBrowse-f815920.html>at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
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> Gmo...@li...
> 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
> 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
>
>


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

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

[Scott C. <sc...@sc...>]

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 <fri...@ho...> wrote:

> Hi Scott,
>
> I attached it
>
> Anja
>
> ------------------------------
> Date: Fri, 1 Oct 2010 06:01:51 -0700
> From: [hidden email]<http://user/SendEmail.jtp?type=node&node=1614664&i=0>
> To: [hidden email] <http://user/SendEmail.jtp?type=node&node=1614664&i=1>
> 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] <http:///user/SendEmail.jtp?type=node&node=1614559&i=0>>
> 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] <http:///user/SendEmail.jtp?type=node&node=1614559&i=1>
> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >
> >
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)  <http://gmod.org/%29%C2%A0>
>          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
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email] <http:///user/SendEmail.jtp?type=node&node=1614559&i=2>
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> ------------------------------
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>
>
>
> *taro.gff* (11K) Download Attachment<http://attachment/1614664/0/taro.gff>
>
> ------------------------------
> View this message in context: RE: 0 features found/no display of data<http://gmod.827538.n3.nabble.com/Gmod-ajax-0-features-found-no-display-of-data-tp1613434p1614664.html>
> Sent from the JBrowse mailing list archive<http://gmod.827538.n3.nabble.com/JBrowse-f815920.html>at Nabble.com.
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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

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

Hi Scott,

I attached it

Anja

Date: Fri, 1 Oct 2010 06:01:51 -0700
From: ml-...@n3...
To: fri...@ho...
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

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

[Scott C. <sc...@sc...>]

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
<fri...@ho...> 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
> Gmo...@li...
> 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

[Gmod-ajax] 0 features found/no display of data

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

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
 		 	   		  

Re: [Gmod-ajax] JBrowse tutorial browser problems in Chrome and Safari (but not Firefox)

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

  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

[Gmod-ajax] JBrowse tutorial browser problems in Chrome and Safari (but not Firefox)

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

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

Re: [Gmod-ajax] auto-complete problem

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

Thanks Mitch,

I indeed think you should add it in the future.
I would also like to remind of the problem with "wrapped" features in GFF of
circular genomes, which are currently simply chopped off.

Keep up the good work,
Dave

On Tue, Sep 28, 2010 at 4:50 PM, Mitch Skinner
<mit...@be...>wrote:

>  Since some data sources (chado, SeqFeature::Store) have IDs which aren't
> meaningful to users, JBrowse currently doesn't do searches on the ID field.
> In the future, we probably should, but for right now you can add an Alias
> tag to your GFF3, something like:
>
> NC_007488       GenBank gene    109368  110333  .       -       1
> ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942;Alias=RSP_3942
>
> And if you have more than one, you can make Alias be a comma-separated
> list:
>
> NC_007488       GenBank gene    109368  110333  .       -       1
> ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942;Alias=RSP_3942,foo,bar
>
> Regards,
> Mitch
>
>
>
> On 09/26/2010 01:53 AM, David Breimann wrote:
>
> Hello,
>
> I have a GFF3 file with lines like:
> NC_007488       GenBank gene    109368  110333  .       -       1
> ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942
> NC_007488       GenBank gene    108526  109371  .       -       1
> ID=RSP_3943;Dbxref=GeneID:3712060;Name=yurM;locus_tag=RSP_3943
>
> I added it using --type=gene --autocomplete=all, then generated names.
> However, I can only look for genes using their names (e.g. yurN) and not
> their IDs or locus_tags.
>
>
> ------------------------------------------------------------------------------
> 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 lis...@li...https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>

Re: [Gmod-ajax] error by runing prepare-refseqs.pl

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

Okay, I think I fixed the problem how to specify the reference sequence. But now I get:

Use of uninitialized value in concatenation (.) or string at bin/prepare-refseqs.pl line 113.
Use of uninitialized value $_ in require at (eval 12) line 1.
Null filename used at (eval 12) line 1.

Anja
Date: Thu, 30 Sep 2010 07:49:57 -0700
From: mit...@be...
To: fri...@ho...
CC: gmo...@li...
Subject: Re: [Gmod-ajax] error by runing prepare-refseqs.pl



  


    
  
  
    On 09/30/2010 02:25 AM, Anja Friedrich wrote:
    
      
      By the way, where did you get the code for the colours in the css
      file from? Wikipedia is using different ones... and can JBrowse
      display any colour? As I have to display 12 small motifs I'm
      running out of colours...

    
    

    JBrowse (technically, the web browser) can display any color, yes. 
    Colors in CSS are hexadecimal numbers; the first third of the digits
    specify the amount of red, the second third specify the amount of
    green, and the last third specify the amount of blue.

    

    So you could specify, say, red with #ff0000, green with #00ff00, and
    blue with #0000ff.  Or, say, a dark red with #550000.  Or whatever
    you wanted.  Most drawing programs will have a tool you can use to
    choose colors, or you could use something like this:

    

    http://www.colorpicker.com/

    

    If you run out of colors, you can also use an image to differentiate
    different motifs; look at the feature, feature2, feature3, feature4,
    and feature5 CSS classes.

    

    Mitch
 		 	   		  

Re: [Gmod-ajax] error by runing prepare-refseqs.pl

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

  On 09/30/2010 02:25 AM, Anja Friedrich wrote:
> By the way, where did you get the code for the colours in the css file 
> from? Wikipedia is using different ones... and can JBrowse display any 
> colour? As I have to display 12 small motifs I'm running out of colours...

JBrowse (technically, the web browser) can display any color, yes.  
Colors in CSS are hexadecimal numbers; the first third of the digits 
specify the amount of red, the second third specify the amount of green, 
and the last third specify the amount of blue.

So you could specify, say, red with #ff0000, green with #00ff00, and 
blue with #0000ff.  Or, say, a dark red with #550000.  Or whatever you 
wanted.  Most drawing programs will have a tool you can use to choose 
colors, or you could use something like this:

http://www.colorpicker.com/

If you run out of colors, you can also use an image to differentiate 
different motifs; look at the feature, feature2, feature3, feature4, and 
feature5 CSS classes.

Mitch

Re: [Gmod-ajax] error by runing prepare-refseqs.pl

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

My bad, I created the config file long time ago and forgot to have alook into it again ;(
By the way, where did you get the code for the colours in the css file from? Wikipedia is using different ones... and can JBrowse display any colour? As I have to display 12 small motifs I'm running out of colours...
Thanks for your help

Anja
Date: Thu, 30 Sep 2010 02:20:44 -0700
From: mit...@be...
To: fri...@ho...
CC: gmo...@li...
Subject: Re: [Gmod-ajax] error by runing prepare-refseqs.pl



  


    
  
  
    You're right that if you use Bio::DB::SeqFeature::Store then you
    don't need to use chado.  But it looks like the config file you're
    using with prepare-refseqs.pl might still refer to
    Bio::DB::Das::Chado?  If you change that to
    Bio::DB::SeqFeature::Store in the config file, then that should
    help.

    

    Mitch

    

    On 09/30/2010 02:13 AM, Anja Friedrich wrote:
    
      
      Hi, 

      

      I loaded the lemna data with bp_seqfeature_load.pl into the
      database and wanted to use bin/prepare-refseqs.pl for the
      reference sequence. But I get:

      

      ------------- EXCEPTION: Bio::Root::Exception -------------

      MSG: unable to find SO or SOFA in the database!

      STACK: Error::throw

      STACK: Bio::Root::Root::throw
      /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368

      STACK: Bio::DB::Das::Chado::sofa_id
      /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482

      STACK: Bio::DB::Das::Chado::new
      /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147

      STACK: bin/prepare-refseqs.pl:115

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

      Could not open database: 

      ------------- EXCEPTION: Bio::Root::Exception -------------

      MSG: unable to find SO or SOFA in the database!

      STACK: Error::throw

      STACK: Bio::Root::Root::throw
      /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368

      STACK: Bio::DB::Das::Chado::sofa_id
      /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482

      STACK: Bio::DB::Das::Chado::new
      /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147

      STACK: bin/prepare-refseqs.pl:115

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

      

      How can that be? I thought if I use Bio-SeqFeature-Store I dont
      need a database like Chado to store the data? Is there somewhere a
      description where I can read more about it and reference
      sequences?

      

      Anja

     		 	   		  

Re: [Gmod-ajax] error by runing prepare-refseqs.pl

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

  You're right that if you use Bio::DB::SeqFeature::Store then you don't 
need to use chado.  But it looks like the config file you're using with 
prepare-refseqs.pl might still refer to Bio::DB::Das::Chado?  If you 
change that to Bio::DB::SeqFeature::Store in the config file, then that 
should help.

Mitch

On 09/30/2010 02:13 AM, Anja Friedrich wrote:
> Hi,
>
> I loaded the lemna data with bp_seqfeature_load.pl into the database 
> and wanted to use bin/prepare-refseqs.pl for the reference sequence. 
> But I get:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: unable to find SO or SOFA in the database!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw 
> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::DB::Das::Chado::sofa_id 
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482
> STACK: Bio::DB::Das::Chado::new 
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147
> STACK: bin/prepare-refseqs.pl:115
> -----------------------------------------------------------
> Could not open database:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: unable to find SO or SOFA in the database!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw 
> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::DB::Das::Chado::sofa_id 
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482
> STACK: Bio::DB::Das::Chado::new 
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147
> STACK: bin/prepare-refseqs.pl:115
> -----------------------------------------------------------
>
> How can that be? I thought if I use Bio-SeqFeature-Store I dont need a 
> database like Chado to store the data? Is there somewhere a 
> description where I can read more about it and reference sequences?
>
> Anja

Re: [Gmod-ajax] error by runing prepare-refseqs.pl

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

Hi, 

I loaded the lemna data with bp_seqfeature_load.pl into the database and wanted to use bin/prepare-refseqs.pl for the reference sequence. But I get:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: unable to find SO or SOFA in the database!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
STACK: Bio::DB::Das::Chado::sofa_id /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482
STACK: Bio::DB::Das::Chado::new /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147
STACK: bin/prepare-refseqs.pl:115
-----------------------------------------------------------
Could not open database: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: unable to find SO or SOFA in the database!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
STACK: Bio::DB::Das::Chado::sofa_id /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482
STACK: Bio::DB::Das::Chado::new /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147
STACK: bin/prepare-refseqs.pl:115
-----------------------------------------------------------

How can that be? I thought if I use Bio-SeqFeature-Store I dont need a database like Chado to store the data? Is there somewhere a description where I can read more about it and reference sequences?

Anja
Date: Wed, 29 Sep 2010 11:29:02 -0700
From: mit...@be...
To: fri...@ho...
CC: gmo...@li...
Subject: Re: [Gmod-ajax] error by runing prepare-refseqs.pl



  


    
    E-Mail-Text
  
  
    Hi,

    

    prepare-refseqs.pl is trying to get a reference sequence
    (chromosome, contig, scaffold, or whatever you have) out of the
    database.  But it's not getting back what it expected to get.

    

    I randomly chose "1" as the name of the reference sequence in the
    example I sent you; I don't know how your reference sequences are
    named.  Are they chromosomes, or scaffolds, or something else?  And
    how are they named?  Is there a reference sequence called "1"?

    

    The intended usage of prepare-refseqs.pl is for you to put a list of
    reference sequence names on the command line, as the values of the
    "--refs" argument.  For example,  if you have 3 scaffolds named
    scaf1, scaf2, and scaf3, your prepare-refseqs.pl command would look
    like this:

    

    bin/prepare-refseqs.pl --conf taro.json --refs scaf1,scaf2,scaf3

    

    In order for that to work, those sequences should already have been
    loaded into your database.

    

    Hope this helps,

    Mitch

    

    On 09/29/2010 07:51 AM, Anja Friedrich wrote:
    
      
      

      

      From: fri...@ho...

      To: gmo...@li...

      Subject: error by runing prepare-refseqs.pl

      Date: Wed, 29 Sep 2010 16:32:22 +0200

      

      
      
      Hi all, 

      

      I tried to run:

      

      >bin/prepare-refseqs.pl --conf taro.json --refs 1

      

      but I get:

      

      Can't call method "name" on an undefined value at
      bin/prepare-refseqs.pl line 72.

      

      Any idea?

      

      Cheers, 

      Anja
      
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