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Re: [Gmod-ajax] Fwd: functions and 9th column attributes

[Cook, M. <ME...@st...>]

I _think_ this is consistent with literal reading of https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md from which:
Column 9: "attributes"
A list of feature attributes in the format tag=value. Multiple tag=value pairs are separated by semicolons. URL escaping rules are used for tags or values containing the following characters: ",=;". Spaces are allowed in this field, but tabs must be replaced with the %09 URL escape. Attribute values do not need to be and should not be quoted. The quotes should be included as part of the value by parsers and not stripped.


From: Colin <col...@gm...>
Sent: Monday, October 01, 2018 12:18 PM
To: Sofia Robb <so...@so...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] Fwd: functions and 9th column attributes

**CAUTION: Non-Stowers email**
It looks like the issue is a space around the semi-colon means that this is included in the attribute name so you can get it by calling

feature.get(" snv.effect")

I don't know what the GFF3 specification says in this case but it does appear that if you removed those spaces it would work too!

-Colin


On Mon, Oct 1, 2018 at 12:56 PM Sofia Robb <so...@so...<mailto:so...@so...>> wrote:
Hi Colin,

Thank you for your reply. I didn't think to try console.log(). Thanks for the tip, but it did not help me clarify my problem. I get undefined when I try console.log('snv.effect') but not console.log('score'). The glyph I tested is one generated from the gff lines below, and the data in the track info window is what it should be, the snv.effect attribute is listed.

Maybe i have done something wrong in my conf file or in my gff:


      {
         "compress" : 0,
         "key" : "SNPs in differential peaks with annotations",
         "label" : "snps_peaks_genes_scores.gff3",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "feature",
            "color" : "function(feature) {console.log(feature.get('snv.effect')) ; return 'red'}"
         },
         "trackType" : "JBrowse/View/Track/CanvasFeatures",
         "type" : "JBrowse/View/Track/CanvasFeatures",
         "urlTemplate" : "tracks/snps_peaks_genes_scores.gff3/{refseq}/trackData.json"
      },

here are a couple of lines from the gff that i loaded:


##gff-version 3
##sequence-region NC_035897.1 17367686 17367798
NC_035897.1 SCI-003279 snv 17367707 17367708 0.225082555874882 . . avg.gerp.gene=NA; avg.gerp.promoter=NA; ensembl.gene=NA; ensembl.tx=NA; motif.genesymbol=KLF10; motif.seq=gagggagCgtgg; peak.bias=surface; peak.padj=0.225082555874882; snv.alt=T; snv.effect=strong; snv.ref=C;_Peak.logfc=0.729035743408939
NC_035897.1 SCI-003279 snv 17367714 17367715 0.225082555874882 . . avg.gerp.gene=NA; avg.gerp.promoter=NA; ensembl.gene=NA; ensembl.tx=NA; motif.genesymbol=ZSCAN22; motif.seq=gagggagggagcgtggagGg; peak.bias=surface; peak.padj=0.225082555874882; snv.alt=A; snv.effect=strong; snv.ref=G;_Peak.logfc=0.729035743408939
###
NC_035897.1 SCI-003279 snv 17367732 17367733 0.225082555874882 . . avg.gerp.gene=NA; avg.gerp.promoter=NA; ensembl.gene=NA; ensembl.tx=NA; motif.genesymbol=RBPJ:Ebox; motif.seq=ctctCggctttttcccc; peak.bias=surface; peak.padj=0.225082555874882; snv.alt=T; snv.effect=strong; snv.ref=C;_Peak.logfc=0.729035743408939
NC_035897.1 SCI-003279 snv 17367742 17367743 0.225082555874882 . . avg.gerp.gene=NA; avg.gerp.promoter=NA; ensembl.gene=NA; ensembl.tx=NA; motif.genesymbol=RFX; motif.seq=ctttttcCccggcaac; peak.bias=surface; peak.padj=0.225082555874882; snv.alt=T; snv.effect=strong; snv.ref=C;_Peak.logfc=0.729035743408939


here is the line I was actually trying to use:
            "color" : "function(feature) {return feature.get('snv.effect')=='strong' ? 'green' : 'blue'}"


Thank you soo much!
Sofia


On Sun, Sep 30, 2018 at 8:33 AM, Colin <col...@gm...<mailto:col...@gm...>> wrote:
I think there is nothing inherently wrong with the attribute name"snp.effect"

You might try console.log the output of feature.get('snv.effect') and see if it helps clarify anything but in my test it seems that it is fine for an attribute to have this in column 9 of a gff (both gff3tabix and flatfile-to-json)

Note that sometimes the color callback is called in children or parent features and then you might have to use feature.parent() or feature.children() and iterate over these

-Colin

On Fri, Sep 28, 2018 at 6:55 PM Sofia Robb <so...@so...<mailto:so...@so...>> wrote:
Hello All,

I am trying to write a function to color my glyph based on a value from one of my 9th column attributes. I can't figure out how to retrieve it.

All my glyphs are blue with this

 "color" : "function(feature) {return feature.get('snv.effect')=='strong' ? 'green' : 'blue'}"


but if i change it to Source it works.

 "color" : "function(feature) {return feature.get('Source')=='strong' ? 'green' : 'blue'}"


Thanks!
Sofia


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Re: [Gmod-ajax] Fwd: functions and 9th column attributes

[Ke J. <bio...@gm...>]

I know spaces are allowed in the fields (values of attributes), just didn't
know it could also be part of the attribute name. I could image this throw
some parsers off.

Thanks for the discussion!

Ke

On Mon, Oct 1, 2018 at 12:56 PM Sofia Robb <so...@so...> wrote:

> Me too!! Say no to whitespace!! :)
>
>
>
> On Mon, Oct 1, 2018 at 11:53 AM, Robert Buels <rb...@gm...> wrote:
>
>> Oh wow nice catch Colin!
>>
>> @Ke, the way I read the spec (
>> https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md),
>> it looks to me like spaces are legal in column 9 according to the spec. But
>> for the reason we see here, I'd not recommend using them!
>>
>> On Mon, Oct 1, 2018 at 10:46 AM Ke Jiang <bio...@gm...> wrote:
>>
>>> So space before attribute name in GFF3 column is legit? I thought that
>>> in a lot of applications/pipelines (ensembl?) that would throw error
>>> messages?
>>>
>>> On Mon, Oct 1, 2018 at 12:34 PM Sofia Robb <so...@so...> wrote:
>>>
>>>> Colin!!!
>>>>
>>>> Ahhh. I noticed the white space and thought, that is was different to
>>>> have so much white space, but I didn't think that could be the
>>>> problem (WHY!!).  Thank you so much! It works beautifully now.
>>>>
>>>> Once again, you are awesome!
>>>> Thanks,
>>>> Sofia
>>>>
>>>>
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>

Re: [Gmod-ajax] Fwd: functions and 9th column attributes

[Sofia R. <so...@so...>]

Me too!! Say no to whitespace!! :)



On Mon, Oct 1, 2018 at 11:53 AM, Robert Buels <rb...@gm...> wrote:

> Oh wow nice catch Colin!
>
> @Ke, the way I read the spec (https://github.com/The-Sequence-Ontology/
> Specifications/blob/master/gff3.md), it looks to me like spaces are legal
> in column 9 according to the spec. But for the reason we see here, I'd not
> recommend using them!
>
> On Mon, Oct 1, 2018 at 10:46 AM Ke Jiang <bio...@gm...> wrote:
>
>> So space before attribute name in GFF3 column is legit? I thought that in
>> a lot of applications/pipelines (ensembl?) that would throw error messages?
>>
>> On Mon, Oct 1, 2018 at 12:34 PM Sofia Robb <so...@so...> wrote:
>>
>>> Colin!!!
>>>
>>> Ahhh. I noticed the white space and thought, that is was different to
>>> have so much white space, but I didn't think that could be the
>>> problem (WHY!!).  Thank you so much! It works beautifully now.
>>>
>>> Once again, you are awesome!
>>> Thanks,
>>> Sofia
>>>
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] Fwd: functions and 9th column attributes

[Robert B. <rb...@gm...>]

Oh wow nice catch Colin!

@Ke, the way I read the spec (
https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md),
it looks to me like spaces are legal in column 9 according to the spec. But
for the reason we see here, I'd not recommend using them!

On Mon, Oct 1, 2018 at 10:46 AM Ke Jiang <bio...@gm...> wrote:

> So space before attribute name in GFF3 column is legit? I thought that in
> a lot of applications/pipelines (ensembl?) that would throw error messages?
>
> On Mon, Oct 1, 2018 at 12:34 PM Sofia Robb <so...@so...> wrote:
>
>> Colin!!!
>>
>> Ahhh. I noticed the white space and thought, that is was different to
>> have so much white space, but I didn't think that could be the
>> problem (WHY!!).  Thank you so much! It works beautifully now.
>>
>> Once again, you are awesome!
>> Thanks,
>> Sofia
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Fwd: functions and 9th column attributes

[Garrett S. <ste...@gm...>]

I'm not sure if some pipelines might throw an error, but according to this
GFF3 spec, spaces are allowed in the 9th column:
https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md


On Mon, Oct 1, 2018 at 1:46 PM Ke Jiang <bio...@gm...> wrote:

> So space before attribute name in GFF3 column is legit? I thought that in
> a lot of applications/pipelines (ensembl?) that would throw error messages?
>
> On Mon, Oct 1, 2018 at 12:34 PM Sofia Robb <so...@so...> wrote:
>
>> Colin!!!
>>
>> Ahhh. I noticed the white space and thought, that is was different to
>> have so much white space, but I didn't think that could be the
>> problem (WHY!!).  Thank you so much! It works beautifully now.
>>
>> Once again, you are awesome!
>> Thanks,
>> Sofia
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Fwd: functions and 9th column attributes

[Ke J. <bio...@gm...>]

So space before attribute name in GFF3 column is legit? I thought that in a
lot of applications/pipelines (ensembl?) that would throw error messages?

On Mon, Oct 1, 2018 at 12:34 PM Sofia Robb <so...@so...> wrote:

> Colin!!!
>
> Ahhh. I noticed the white space and thought, that is was different to have
> so much white space, but I didn't think that could be the problem (WHY!!).
> Thank you so much! It works beautifully now.
>
> Once again, you are awesome!
> Thanks,
> Sofia
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Fwd: functions and 9th column attributes

[Sofia R. <so...@so...>]

Colin!!!

Ahhh. I noticed the white space and thought, that is was different to have
so much white space, but I didn't think that could be the problem (WHY!!).
Thank you so much! It works beautifully now.

Once again, you are awesome!
Thanks,
Sofia

Re: [Gmod-ajax] Fwd: functions and 9th column attributes

[Colin <col...@gm...>]

It looks like the issue is a space around the semi-colon means that this is
included in the attribute name so you can get it by calling

feature.get(" snv.effect")

I don't know what the GFF3 specification says in this case but it does
appear that if you removed those spaces it would work too!

-Colin


On Mon, Oct 1, 2018 at 12:56 PM Sofia Robb <so...@so...> wrote:

> Hi Colin,
>
> Thank you for your reply. I didn't think to try console.log(). Thanks for
> the tip, but it did not help me clarify my problem. I get undefined when I
> try console.log('snv.effect') but not console.log('score'). The glyph I
> tested is one generated from the gff lines below, and the data in the track
> info window is what it should be, the snv.effect attribute is listed.
>
> Maybe i have done something wrong in my conf file or in my gff:
>
>
>       {
>          "compress" : 0,
>          "key" : "SNPs in differential peaks with annotations",
>          "label" : "snps_peaks_genes_scores.gff3",
>          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
>          "style" : {
>             "className" : "feature",
>             "color" : "function(feature)
> {console.log(feature.get('snv.effect')) ; return 'red'}"
>          },
>          "trackType" : "JBrowse/View/Track/CanvasFeatures",
>          "type" : "JBrowse/View/Track/CanvasFeatures",
>          "urlTemplate" :
> "tracks/snps_peaks_genes_scores.gff3/{refseq}/trackData.json"
>       },
>
> here are a couple of lines from the gff that i loaded:
>
>
> ##gff-version 3
> ##sequence-region NC_035897.1 17367686 17367798
> NC_035897.1 SCI-003279 snv 17367707 17367708 0.225082555874882 . . avg.gerp.gene=NA;
> avg.gerp.promoter=NA; ensembl.gene=NA; ensembl.tx=NA;
> motif.genesymbol=KLF10; motif.seq=gagggagCgtgg; peak.bias=surface;
> peak.padj=0.225082555874882; snv.alt=T; snv.effect=strong;
> snv.ref=C;_Peak.logfc=0.729035743408939
> NC_035897.1 SCI-003279 snv 17367714 17367715 0.225082555874882 . . avg.gerp.gene=NA;
> avg.gerp.promoter=NA; ensembl.gene=NA; ensembl.tx=NA;
> motif.genesymbol=ZSCAN22; motif.seq=gagggagggagcgtggagGg;
> peak.bias=surface; peak.padj=0.225082555874882; snv.alt=A;
> snv.effect=strong; snv.ref=G;_Peak.logfc=0.729035743408939
> ###
> NC_035897.1 SCI-003279 snv 17367732 17367733 0.225082555874882 . . avg.gerp.gene=NA;
> avg.gerp.promoter=NA; ensembl.gene=NA; ensembl.tx=NA;
> motif.genesymbol=RBPJ:Ebox; motif.seq=ctctCggctttttcccc; peak.bias=surface;
> peak.padj=0.225082555874882; snv.alt=T; snv.effect=strong;
> snv.ref=C;_Peak.logfc=0.729035743408939
> NC_035897.1 SCI-003279 snv 17367742 17367743 0.225082555874882 . . avg.gerp.gene=NA;
> avg.gerp.promoter=NA; ensembl.gene=NA; ensembl.tx=NA; motif.genesymbol=RFX;
> motif.seq=ctttttcCccggcaac; peak.bias=surface; peak.padj=0.225082555874882;
> snv.alt=T; snv.effect=strong; snv.ref=C;_Peak.logfc=0.729035743408939
>
>
> here is the line I was actually trying to use:
>             "color" : "function(feature) {return
> feature.get('snv.effect')=='strong' ? 'green' : 'blue'}"
>
>
> Thank you soo much!
> Sofia
>
>
> On Sun, Sep 30, 2018 at 8:33 AM, Colin <col...@gm...> wrote:
>
>> I think there is nothing inherently wrong with the attribute
>> name"snp.effect"
>>
>> You might try console.log the output of feature.get('snv.effect') and see
>> if it helps clarify anything but in my test it seems that it is fine for an
>> attribute to have this in column 9 of a gff (both gff3tabix and
>> flatfile-to-json)
>>
>> Note that sometimes the color callback is called in children or parent
>> features and then you might have to use feature.parent() or
>> feature.children() and iterate over these
>>
>> -Colin
>>
>> On Fri, Sep 28, 2018 at 6:55 PM Sofia Robb <so...@so...> wrote:
>>
>>> Hello All,
>>>
>>> I am trying to write a function to color my glyph based on a value from
>>> one of my 9th column attributes. I can't figure out how to retrieve it.
>>>
>>> All my glyphs are blue with this
>>>
>>>  "color" : "function(feature) {return
>>> feature.get('snv.effect')=='strong' ? 'green' : 'blue'}"
>>>
>>>
>>> but if i change it to Source it works.
>>>
>>>  "color" : "function(feature) {return feature.get('Source')=='strong' ?
>>> 'green' : 'blue'}"
>>>
>>>
>>> Thanks!
>>> Sofia
>>>
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>

Re: [Gmod-ajax] local autoscale for coverage depth in Alignments2 tracks

[Colin <col...@gm...>]

The coverage that is displayed using the histograms is implemented
differently from a normal XYPlot, so there is less configuration available.
But what does happen is that it gets "stats" from the bigwig store if you
have the bigwig histogram configured, and then uses "stats.max" so it
should be similar to autoscale=global. That "stats.max" is different for
each refseq. If you want it the same globally across all refseqs you can
manually set "histograms.max" in the config

-Colin

On Mon, Oct 1, 2018 at 10:51 AM Loraine Guéguen <
lor...@sb...> wrote:

> But how is set the default scale for he coverage depth histogram of the
> Alignments2 track ? "autoscale"="global" ?
> It seems to depend on the data (different scale for different track) but
> not on the zoom level.
>
>
>
> Le 01/10/2018 09:42, Loraine Guéguen a écrit :
>
> ok, I have added a comment in the GitHub issue.
> Thanks
>
> Le 30/09/2018 16:48, Colin a écrit :
>
> The only thing I can really say is to stay tuned to the GitHub issue :) If
> it has a github issue that has stayed open it is likely still on our radar
>
>
> -Colin
>
> On Fri, Sep 28, 2018 at 11:28 AM Loraine Guéguen <
> lor...@sb...> wrote:
>
>> Dear JBrowse team and list,
>>
>> The same Bigwig file in a track of type XYPlot and in a track of type
>> Alignments2 (BAM display) with the coverage depth histogram is not
>> displayed with the same scale. Whereas the scale in the XYPlot track
>> looks fine (with autoscale=local), the scale in the coverage depth of
>> the Alignments2 track is not suitable (too big).
>>
>> How is set the display scale for the coverage depth of the Alignments2
>> track ?
>> I would like to set "autoscale"="local" as in XYPlot tracks, but it
>> seems it is not working (because of
>> https://github.com/GMOD/jbrowse/issues/1164#issuecomment-410875923 ?)
>>
>> Thanks,
>>
>> Loraine Guéguen
>>
>> --
>> Loraine Guéguen
>>
>> UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
>> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
>>
>> Station Biologique de Roscoff - CNRS | Sorbonne Université
>> Place Georges Teissier - CS 90074
>> 29688 Roscoff cedex
>> tel: ++33 (0)2 98 29 56 46 (interne : 415)
>> http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
>> http://abims.sb-roscoff.fr/
>>
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
> --
> Loraine Guéguen
>
> UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
>
> Station Biologique de Roscoff - CNRS | Sorbonne Université
> Place Georges Teissier - CS 90074
> 29688 Roscoff cedex
> tel: ++33 (0)2 98 29 56 46 (interne : 415)http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-modelshttp://abims.sb-roscoff.fr/
>
>
>
>
>
> _______________________________________________
> Gmod-ajax mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> --
> Loraine Guéguen
>
> UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
>
> Station Biologique de Roscoff - CNRS | Sorbonne Université
> Place Georges Teissier - CS 90074
> 29688 Roscoff cedex
> tel: ++33 (0)2 98 29 56 46 (interne : 415)http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-modelshttp://abims.sb-roscoff.fr/
>
>

Re: [Gmod-ajax] Fwd: functions and 9th column attributes

[Sofia R. <so...@so...>]

Hi Colin,

Thank you for your reply. I didn't think to try console.log(). Thanks for
the tip, but it did not help me clarify my problem. I get undefined when I
try console.log('snv.effect') but not console.log('score'). The glyph I
tested is one generated from the gff lines below, and the data in the track
info window is what it should be, the snv.effect attribute is listed.

Maybe i have done something wrong in my conf file or in my gff:


      {
         "compress" : 0,
         "key" : "SNPs in differential peaks with annotations",
         "label" : "snps_peaks_genes_scores.gff3",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "feature",
            "color" : "function(feature)
{console.log(feature.get('snv.effect')) ; return 'red'}"
         },
         "trackType" : "JBrowse/View/Track/CanvasFeatures",
         "type" : "JBrowse/View/Track/CanvasFeatures",
         "urlTemplate" :
"tracks/snps_peaks_genes_scores.gff3/{refseq}/trackData.json"
      },

here are a couple of lines from the gff that i loaded:


##gff-version 3
##sequence-region NC_035897.1 17367686 17367798
NC_035897.1 SCI-003279 snv 17367707 17367708 0.225082555874882 . .
avg.gerp.gene=NA;
avg.gerp.promoter=NA; ensembl.gene=NA; ensembl.tx=NA;
motif.genesymbol=KLF10; motif.seq=gagggagCgtgg; peak.bias=surface;
peak.padj=0.225082555874882; snv.alt=T; snv.effect=strong;
snv.ref=C;_Peak.logfc=0.729035743408939
NC_035897.1 SCI-003279 snv 17367714 17367715 0.225082555874882 . .
avg.gerp.gene=NA;
avg.gerp.promoter=NA; ensembl.gene=NA; ensembl.tx=NA;
motif.genesymbol=ZSCAN22; motif.seq=gagggagggagcgtggagGg;
peak.bias=surface; peak.padj=0.225082555874882; snv.alt=A;
snv.effect=strong; snv.ref=G;_Peak.logfc=0.729035743408939
###
NC_035897.1 SCI-003279 snv 17367732 17367733 0.225082555874882 . .
avg.gerp.gene=NA;
avg.gerp.promoter=NA; ensembl.gene=NA; ensembl.tx=NA;
motif.genesymbol=RBPJ:Ebox; motif.seq=ctctCggctttttcccc; peak.bias=surface;
peak.padj=0.225082555874882; snv.alt=T; snv.effect=strong;
snv.ref=C;_Peak.logfc=0.729035743408939
NC_035897.1 SCI-003279 snv 17367742 17367743 0.225082555874882 . .
avg.gerp.gene=NA;
avg.gerp.promoter=NA; ensembl.gene=NA; ensembl.tx=NA; motif.genesymbol=RFX;
motif.seq=ctttttcCccggcaac; peak.bias=surface; peak.padj=0.225082555874882;
snv.alt=T; snv.effect=strong; snv.ref=C;_Peak.logfc=0.729035743408939


here is the line I was actually trying to use:
            "color" : "function(feature) {return
feature.get('snv.effect')=='strong' ? 'green' : 'blue'}"


Thank you soo much!
Sofia


On Sun, Sep 30, 2018 at 8:33 AM, Colin <col...@gm...> wrote:

> I think there is nothing inherently wrong with the attribute
> name"snp.effect"
>
> You might try console.log the output of feature.get('snv.effect') and see
> if it helps clarify anything but in my test it seems that it is fine for an
> attribute to have this in column 9 of a gff (both gff3tabix and
> flatfile-to-json)
>
> Note that sometimes the color callback is called in children or parent
> features and then you might have to use feature.parent() or
> feature.children() and iterate over these
>
> -Colin
>
> On Fri, Sep 28, 2018 at 6:55 PM Sofia Robb <so...@so...> wrote:
>
>> Hello All,
>>
>> I am trying to write a function to color my glyph based on a value from
>> one of my 9th column attributes. I can't figure out how to retrieve it.
>>
>> All my glyphs are blue with this
>>
>>  "color" : "function(feature) {return feature.get('snv.effect')=='strong'
>> ? 'green' : 'blue'}"
>>
>>
>> but if i change it to Source it works.
>>
>>  "color" : "function(feature) {return feature.get('Source')=='strong' ?
>> 'green' : 'blue'}"
>>
>>
>> Thanks!
>> Sofia
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] local autoscale for coverage depth in Alignments2 tracks

[Loraine G. <lor...@sb...>]

But how is set the default scale for he coverage depth histogram of the 
Alignments2 track ? "autoscale"="global" ?
It seems to depend on the data (different scale for different track) but 
not on the zoom level.



Le 01/10/2018 09:42, Loraine Guéguen a écrit :
> ok, I have added a comment in the GitHub issue.
> Thanks
>
> Le 30/09/2018 16:48, Colin a écrit :
>> The only thing I can really say is to stay tuned to the GitHub issue 
>> :) If it has a github issue that has stayed open it is likely still 
>> on our radar
>>
>>
>> -Colin
>>
>> On Fri, Sep 28, 2018 at 11:28 AM Loraine Guéguen 
>> <lor...@sb... 
>> <mailto:lor...@sb...>> wrote:
>>
>>     Dear JBrowse team and list,
>>
>>     The same Bigwig file in a track of type XYPlot and in a track of
>>     type
>>     Alignments2 (BAM display) with the coverage depth histogram is not
>>     displayed with the same scale. Whereas the scale in the XYPlot track
>>     looks fine (with autoscale=local), the scale in the coverage
>>     depth of
>>     the Alignments2 track is not suitable (too big).
>>
>>     How is set the display scale for the coverage depth of the
>>     Alignments2
>>     track ?
>>     I would like to set "autoscale"="local" as in XYPlot tracks, but it
>>     seems it is not working (because of
>>     https://github.com/GMOD/jbrowse/issues/1164#issuecomment-410875923 ?)
>>
>>     Thanks,
>>
>>     Loraine Guéguen
>>
>>     -- 
>>     Loraine Guéguen
>>
>>     UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
>>     Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
>>
>>     Station Biologique de Roscoff - CNRS | Sorbonne Université
>>     Place Georges Teissier - CS 90074
>>     29688 Roscoff cedex
>>     tel: ++33 (0)2 98 29 56 46 (interne : 415)
>>     http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
>>     http://abims.sb-roscoff.fr/
>>
>>
>>
>>     _______________________________________________
>>     Gmod-ajax mailing list
>>     Gmo...@li...
>>     <mailto:Gmo...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
> -- 
> Loraine Guéguen
>
> UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
>
> Station Biologique de Roscoff - CNRS | Sorbonne Université
> Place Georges Teissier - CS 90074
> 29688 Roscoff cedex
> tel: ++33 (0)2 98 29 56 46 (interne : 415)
> http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
> http://abims.sb-roscoff.fr/
>
>
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

-- 
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS | Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/

Re: [Gmod-ajax] local autoscale for coverage depth in Alignments2 tracks

[Loraine G. <lor...@sb...>]

ok, I have added a comment in the GitHub issue.
Thanks

Le 30/09/2018 16:48, Colin a écrit :
> The only thing I can really say is to stay tuned to the GitHub issue 
> :) If it has a github issue that has stayed open it is likely still on 
> our radar
>
>
> -Colin
>
> On Fri, Sep 28, 2018 at 11:28 AM Loraine Guéguen 
> <lor...@sb... <mailto:lor...@sb...>> 
> wrote:
>
>     Dear JBrowse team and list,
>
>     The same Bigwig file in a track of type XYPlot and in a track of type
>     Alignments2 (BAM display) with the coverage depth histogram is not
>     displayed with the same scale. Whereas the scale in the XYPlot track
>     looks fine (with autoscale=local), the scale in the coverage depth of
>     the Alignments2 track is not suitable (too big).
>
>     How is set the display scale for the coverage depth of the
>     Alignments2
>     track ?
>     I would like to set "autoscale"="local" as in XYPlot tracks, but it
>     seems it is not working (because of
>     https://github.com/GMOD/jbrowse/issues/1164#issuecomment-410875923 ?)
>
>     Thanks,
>
>     Loraine Guéguen
>
>     -- 
>     Loraine Guéguen
>
>     UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
>     Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
>
>     Station Biologique de Roscoff - CNRS | Sorbonne Université
>     Place Georges Teissier - CS 90074
>     29688 Roscoff cedex
>     tel: ++33 (0)2 98 29 56 46 (interne : 415)
>     http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
>     http://abims.sb-roscoff.fr/
>
>
>
>     _______________________________________________
>     Gmod-ajax mailing list
>     Gmo...@li...
>     <mailto:Gmo...@li...>
>     https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

-- 
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS | Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/

Re: [Gmod-ajax] local autoscale for coverage depth in Alignments2 tracks

[Colin <col...@gm...>]

The only thing I can really say is to stay tuned to the GitHub issue :) If
it has a github issue that has stayed open it is likely still on our radar


-Colin

On Fri, Sep 28, 2018 at 11:28 AM Loraine Guéguen <
lor...@sb...> wrote:

> Dear JBrowse team and list,
>
> The same Bigwig file in a track of type XYPlot and in a track of type
> Alignments2 (BAM display) with the coverage depth histogram is not
> displayed with the same scale. Whereas the scale in the XYPlot track
> looks fine (with autoscale=local), the scale in the coverage depth of
> the Alignments2 track is not suitable (too big).
>
> How is set the display scale for the coverage depth of the Alignments2
> track ?
> I would like to set "autoscale"="local" as in XYPlot tracks, but it
> seems it is not working (because of
> https://github.com/GMOD/jbrowse/issues/1164#issuecomment-410875923 ?)
>
> Thanks,
>
> Loraine Guéguen
>
> --
> Loraine Guéguen
>
> UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
>
> Station Biologique de Roscoff - CNRS | Sorbonne Université
> Place Georges Teissier - CS 90074
> 29688 Roscoff cedex
> tel: ++33 (0)2 98 29 56 46 (interne : 415)
> http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
> http://abims.sb-roscoff.fr/
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Fwd: functions and 9th column attributes

[Colin <col...@gm...>]

I think there is nothing inherently wrong with the attribute
name"snp.effect"

You might try console.log the output of feature.get('snv.effect') and see
if it helps clarify anything but in my test it seems that it is fine for an
attribute to have this in column 9 of a gff (both gff3tabix and
flatfile-to-json)

Note that sometimes the color callback is called in children or parent
features and then you might have to use feature.parent() or
feature.children() and iterate over these

-Colin

On Fri, Sep 28, 2018 at 6:55 PM Sofia Robb <so...@so...> wrote:

> Hello All,
>
> I am trying to write a function to color my glyph based on a value from
> one of my 9th column attributes. I can't figure out how to retrieve it.
>
> All my glyphs are blue with this
>
>  "color" : "function(feature) {return feature.get('snv.effect')=='strong'
> ? 'green' : 'blue'}"
>
>
> but if i change it to Source it works.
>
>  "color" : "function(feature) {return feature.get('Source')=='strong' ?
> 'green' : 'blue'}"
>
>
> Thanks!
> Sofia
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Fwd: functions and 9th column attributes

[Sofia R. <so...@so...>]

Hello All,

I am trying to write a function to color my glyph based on a value from one
of my 9th column attributes. I can't figure out how to retrieve it.

All my glyphs are blue with this

 "color" : "function(feature) {return feature.get('snv.effect')=='strong' ?
'green' : 'blue'}"


but if i change it to Source it works.

 "color" : "function(feature) {return feature.get('Source')=='strong' ?
'green' : 'blue'}"


Thanks!
Sofia

[Gmod-ajax] local autoscale for coverage depth in Alignments2 tracks

[Loraine G. <lor...@sb...>]

Dear JBrowse team and list,

The same Bigwig file in a track of type XYPlot and in a track of type 
Alignments2 (BAM display) with the coverage depth histogram is not 
displayed with the same scale. Whereas the scale in the XYPlot track 
looks fine (with autoscale=local), the scale in the coverage depth of 
the Alignments2 track is not suitable (too big).

How is set the display scale for the coverage depth of the Alignments2 
track ?
I would like to set "autoscale"="local" as in XYPlot tracks, but it 
seems it is not working (because of 
https://github.com/GMOD/jbrowse/issues/1164#issuecomment-410875923 ?)

Thanks,

Loraine Guéguen

-- 
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS | Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/

Re: [Gmod-ajax] algorithm

[Nathan D. <nat...@lb...>]

I would review these docs: 

http://jbrowse.org/docs/plugins.html#writing-jbrowse-plugins

And these examples:

https://gmod.github.io/jbrowse-registry/

Cheers,

Nathan


> On Sep 23, 2018, at 12:16 AM, Anubhav Roy <anu...@gm...> wrote:
> 
> kindly tell me the entire algorithm behind jbrowse plugins
> thank you
> 
> -- 
> Anubhav Roy
> Ph.D. (Bioinformatics)
> IASRI, Pusa, New delhi - 110012
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] algorithm

[Anubhav R. <anu...@gm...>]

kindly tell me the entire algorithm behind jbrowse plugins
thank you

-- 
Anubhav Roy
Ph.D. (Bioinformatics)
IASRI, Pusa, New delhi - 110012

Re: [Gmod-ajax] plugin installation

[Colin <col...@gm...>]

Receiving an error status code 0 from a file is weird. Can you open the
"console" and see if this says anything? Right-click the webpage and click
Inspect Element and then go to the console tab


-Colin

On Fri, Sep 21, 2018 at 4:09 PM Anubhav Roy <anu...@gm...>
wrote:

> after adding those two lines when i tried to open jbrowse is says the
> following in the attachment
>
> On Sat, Sep 22, 2018 at 1:36 AM Anubhav Roy <anu...@gm...>
> wrote:
>
>> see in this conf file  in teh section which starts with "## uncomment and
>> edit the example below to enable one or more.." i added the below mentioned
>> two lines as said by author
>> [ plugins.TrackScorePlugin ]
>>
>> location = plugins/TrackScorePlugin
>>
>>
>>
>> On Sep 22, 2018 1:02 AM, "Colin" <col...@gm...> wrote:
>>
>>> Hi there
>>>
>>> The attachment you posted lists the installation steps in detail!
>>>
>>> If you can post your config files and steps that you have tried maybe we
>>> can help
>>>
>>>
>>>
>>> -Colin
>>>
>>> On Fri, Sep 21, 2018 at 1:48 PM Anubhav Roy <anu...@gm...>
>>> wrote:
>>>
>>>> I have installed a plugin but i failed to activate it. i did
>>>> accordingly as it is said by author but it didnt work i am sending the
>>>> screenshot of the procedure. tell me in detail specially the adding portion
>>>> in jbrowse.conf file.
>>>> regards
>>>>
>>>> --
>>>> Anubhav Roy
>>>> Ph.D. (Bioinformatics)
>>>> IASRI, Pusa, New delhi - 110012
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>
>
> --
> Anubhav Roy
> Ph.D. (Bioinformatics)
> IASRI, Pusa, New delhi - 110012
>

Re: [Gmod-ajax] plugin installation

[Anubhav R. <anu...@gm...>]

see in this conf file  in teh section which starts with "## uncomment and
edit the example below to enable one or more.." i added the below mentioned
two lines as said by author
[ plugins.TrackScorePlugin ]

location = plugins/TrackScorePlugin



On Sep 22, 2018 1:02 AM, "Colin" <col...@gm...> wrote:

> Hi there
>
> The attachment you posted lists the installation steps in detail!
>
> If you can post your config files and steps that you have tried maybe we
> can help
>
>
>
> -Colin
>
> On Fri, Sep 21, 2018 at 1:48 PM Anubhav Roy <anu...@gm...>
> wrote:
>
>> I have installed a plugin but i failed to activate it. i did accordingly
>> as it is said by author but it didnt work i am sending the screenshot of
>> the procedure. tell me in detail specially the adding portion in
>> jbrowse.conf file.
>> regards
>>
>> --
>> Anubhav Roy
>> Ph.D. (Bioinformatics)
>> IASRI, Pusa, New delhi - 110012
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] plugin installation

[Colin <col...@gm...>]

Hi there

The attachment you posted lists the installation steps in detail!

If you can post your config files and steps that you have tried maybe we
can help



-Colin

On Fri, Sep 21, 2018 at 1:48 PM Anubhav Roy <anu...@gm...>
wrote:

> I have installed a plugin but i failed to activate it. i did accordingly
> as it is said by author but it didnt work i am sending the screenshot of
> the procedure. tell me in detail specially the adding portion in
> jbrowse.conf file.
> regards
>
> --
> Anubhav Roy
> Ph.D. (Bioinformatics)
> IASRI, Pusa, New delhi - 110012
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] (no subject)

[Colin <col...@gm...>]

The JSON format uses curly braces, so an empty JSON is just

{
}

I believe you have parentheses pictured

-Colin

On Fri, Sep 21, 2018 at 1:12 PM Anubhav Roy <anu...@gm...>
wrote:

> thsi is the jbrowse_conf.json file.kindly check
>
> On Sep 21, 2018 10:01 PM, "Colin" <col...@gm...> wrote:
>
>> Can you post jbrowse_conf.json? It says there is a syntax error in this
>> file
>>
>> -Colin
>>
>> On Fri, Sep 21, 2018 at 12:16 PM Anubhav Roy <anu...@gm...>
>> wrote:
>>
>>> volvox example data is not opening in browser though i have successfully
>>> installed and run setup.sh file .i have also installed lampp web
>>> server.please help.SCREENSHOT and SET.LOG are ATTACHED.
>>> --
>>> Anubhav Roy
>>> Ph.D. (Bioinformatics)
>>> IASRI, Pusa, New delhi - 110012
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>

[Gmod-ajax] plugin installation

[Anubhav R. <anu...@gm...>]

I have installed a plugin but i failed to activate it. i did accordingly as
it is said by author but it didnt work i am sending the screenshot of the
procedure. tell me in detail specially the adding portion in jbrowse.conf
file.
regards

-- 
Anubhav Roy
Ph.D. (Bioinformatics)
IASRI, Pusa, New delhi - 110012

Re: [Gmod-ajax] (no subject)

[Anubhav R. <anu...@gm...>]

thsi is the jbrowse_conf.json file.kindly check

On Sep 21, 2018 10:01 PM, "Colin" <col...@gm...> wrote:

> Can you post jbrowse_conf.json? It says there is a syntax error in this
> file
>
> -Colin
>
> On Fri, Sep 21, 2018 at 12:16 PM Anubhav Roy <anu...@gm...>
> wrote:
>
>> volvox example data is not opening in browser though i have successfully
>> installed and run setup.sh file .i have also installed lampp web
>> server.please help.SCREENSHOT and SET.LOG are ATTACHED.
>> --
>> Anubhav Roy
>> Ph.D. (Bioinformatics)
>> IASRI, Pusa, New delhi - 110012
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] (no subject)

[Colin <col...@gm...>]

Can you post jbrowse_conf.json? It says there is a syntax error in this file

-Colin

On Fri, Sep 21, 2018 at 12:16 PM Anubhav Roy <anu...@gm...>
wrote:

> volvox example data is not opening in browser though i have successfully
> installed and run setup.sh file .i have also installed lampp web
> server.please help.SCREENSHOT and SET.LOG are ATTACHED.
> --
> Anubhav Roy
> Ph.D. (Bioinformatics)
> IASRI, Pusa, New delhi - 110012
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>