gmod-ajax — JBrowse list

[Gmod-ajax] JBrowse 1.15.2 released

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

Hi all,


JBrowse 1.15.2 has been released! This contains a couple nice features
including estimating feature density directly from the index file of BAM,
VCF, and other tabix formats. We also updated the website with a new
blogging and documentation platform! Please try it out and give us feedback.

Enjoy browsing!

   - JBrowse-1.15.2.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2.zip>
-
   4.34 MB
   - JBrowse-1.15.2-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-win32-x64.zip>
-
   69M
   - JBrowse-1.15.2-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-linux-x64.zip>
-
   67M
   - JBrowse-1.15.2-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-darwin-x64.zip>
-
   68M

<http://localhost:3000/blog/#minor-improvements>Minor improvements

   -

   Created "index stats estimation" which overrides the older "global stats
   estimation" that randomly samples genomic regions of BAM, VCF, etc to find
   feature density. This allows initial track load to be faster automatically.
   (issue #1092 <https://github.com/gmod/jbrowse/issues/1092>, issue #1167
   <https://github.com/gmod/jbrowse/pull/1167>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Removed the "full" or "dev" releases from the build. If you need a "dev"
   release, you can simply download the JBrowse "source code" link from the
   GitHub releases page, or use a git clone of the JBrowse repository. This
   will behave the same as the "dev" release. (issue #1160
   <https://github.com/gmod/jbrowse/issues/1160>, issue #1170
   <https://github.com/gmod/jbrowse/pull/1170>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   JBrowse now uses a new binary-file caching and fetching backend based on
   the http-range-fetcher <https://www.npmjs.com/package/http-range-fetcher>
    andtenacious-fetch <https://www.npmjs.com/package/tenacious-fetch> npm
   modules. Users may see slightly higher performance when viewing indexed
   binary formats such as BAM, CRAM, 2bit, etc. (issue #1155
   <https://github.com/gmod/jbrowse/issues/1155>, issue #1175
   <https://github.com/gmod/jbrowse/issues/1175>, issue #1165
   <https://github.com/gmod/jbrowse/pull/1165>, @rbuels
   <https://github.com/rbuels>)
   -

   Updated the main jbrowse.org website to use the docusaurus platform. The
   main docs for the website are now moved from the GMOD.org server to
   jbrowse.org. You can find the latest documentation in the header bar. We
   hope you will enjoy this upgrade! There is also a new quick start guide
   based on setting up JBrowse with indexed file formats. (issue #1153
   <https://github.com/gmod/jbrowse/issues/1153>, issue #1137
   <https://github.com/gmod/jbrowse/issues/1137>, issue #1173
   <https://github.com/gmod/jbrowse/pull/1173>, @cmdcolin
   <https://github.com/cmdcolin>)

<http://localhost:3000/blog/#bug-fixes>Bug fixes

   -

   Added a more robust HTML processing in Util.js. Thanks to @hkmoon
   <https://github.com/hkmoon> for the idea and implementation. (issue #1169
   <https://github.com/gmod/jbrowse/pull/1169>, @hkmoon
   <https://github.com/hkmoon>)
   -

   Remove utils/jb_run.js from the minified release (issue #1161
   <https://github.com/gmod/jbrowse/issues/1161>, issue #1160
   <https://github.com/gmod/jbrowse/issues/1160>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixes issue where navigating away from genome browser and returning
   would not remember the location. Thanks to Vaneet Lotay for
reporting. (issue
   #1168 <https://github.com/gmod/jbrowse/issues/1168>, @cmdcolin
   <https://github.com/cmdcolin>)
   -

   Fixes off-by-one in the display of the size of the genomic region being
   viewed. Thanks to @sammyjava <https://github.com/sammyjava>for the bug
   report! (issue #1176 <https://github.com/gmod/jbrowse/issues/1176>,
   @cmdcolin <https://github.com/cmdcolin>)

Re: [Gmod-ajax] JBrowse cached location/coordinates not working

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

Hi Vaneet,

I identified the issue and put in a fix! Will be released in the next
version! https://github.com/GMOD/jbrowse/issues/1168

The source code fix isn't too complex if you need to add it into your
current version too

https://github.com/GMOD/jbrowse/commit/29043f40e81a88bcc39a781a32ff39fc7abbe9c2

-Colin

On Wed, Aug 8, 2018 at 5:57 PM Colin <col...@gm...> wrote:

> I think a specific thing that would help is knowing your dataset selector
> configuration
>
> -Colin
>
> On Wed, Aug 8, 2018, 5:42 PM Vaneet Lotay <van...@uc...>
> wrote:
>
>> Hello,
>>
>>
>>
>> I noticed when I switched between genomes using the dataset selector that
>> it doesn’t come back to the same location or the same gene I was looking
>> at, it goes to a different chromosome and different coordinates all
>> together.  I’ve seen this issue no matter which genome I go to the second
>> time around, the only thing that’s always the same is that it’s always in a
>> viewing window that’s zoomed out to a significant amount and appears to be
>> always the same Chromosome and coordinates (not the ones I was viewing
>> previously).
>>
>>
>>
>> I can send you links to my instance directly if you want to see the issue
>> I’m talking about.  This is version JBrowse 1.14.2-dev.  I’ve tried it both
>> in Chrome and Firefox, same issue.
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Vaneet
>>
>>
>>
>>
>>
>> *Vaneet Lotay*
>>
>> *Xenbase Bioinformatician*
>>
>> *716 ICT Building - University of Calgary*
>>
>> *2500 University Drive NW*
>>
>> *Calgary AB T2N 1N4*
>>
>> *CANADA*
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] Control Ordering of Categories in Left-hand Panel?

[Ben B. <bb...@gm...>]

i think that should be able to work, thanks.

On Tue, Aug 14, 2018 at 12:46 PM Colin <col...@gm...> wrote:

> There is no way to provide a custom sort function currently but you can
> specify "trackSelector.sortHierarchical=false" and then the sorting will be
> basically in whichever order the tracks are loaded as. If that does not
> satisfy the issue, as in maybe you do need a custom sorter besides "no
> sorting", feel free to make a github issue
>
> In jbrowse.conf that might look like
>
> [trackSelector]
> sortHierarchical=false
>
>
> Or in trackList.json
>
> "trackSelector": {
>     "sortHierarchical": false
> }
>
> -Colin
>
> On Tue, Aug 14, 2018 at 3:36 PM Ben Bimber <bb...@gm...> wrote:
>
>> Hello,
>>
>> In a jbrowse session, you provide a list of tracks, and these tracks can
>> have a category.  The left-hand panel shows available tracks, with tracks
>> grouped by category.  It seems to sort categories alphabetically.  is it
>> possible to manually provide a sort order for categories in one of the JSON
>> contig files?  I didnt see anything like this in the examples:
>> http://gmod.org/wiki/JBrowse_Configuration_Guide.
>>
>> Thanks for any help,
>> Ben
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] Control Ordering of Categories in Left-hand Panel?

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

There is no way to provide a custom sort function currently but you can
specify "trackSelector.sortHierarchical=false" and then the sorting will be
basically in whichever order the tracks are loaded as. If that does not
satisfy the issue, as in maybe you do need a custom sorter besides "no
sorting", feel free to make a github issue

In jbrowse.conf that might look like

[trackSelector]
sortHierarchical=false


Or in trackList.json

"trackSelector": {
    "sortHierarchical": false
}

-Colin

On Tue, Aug 14, 2018 at 3:36 PM Ben Bimber <bb...@gm...> wrote:

> Hello,
>
> In a jbrowse session, you provide a list of tracks, and these tracks can
> have a category.  The left-hand panel shows available tracks, with tracks
> grouped by category.  It seems to sort categories alphabetically.  is it
> possible to manually provide a sort order for categories in one of the JSON
> contig files?  I didnt see anything like this in the examples:
> http://gmod.org/wiki/JBrowse_Configuration_Guide.
>
> Thanks for any help,
> Ben
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Control Ordering of Categories in Left-hand Panel?

[Ben B. <bb...@gm...>]

Hello,

In a jbrowse session, you provide a list of tracks, and these tracks can
have a category.  The left-hand panel shows available tracks, with tracks
grouped by category.  It seems to sort categories alphabetically.  is it
possible to manually provide a sort order for categories in one of the JSON
contig files?  I didnt see anything like this in the examples:
http://gmod.org/wiki/JBrowse_Configuration_Guide.

Thanks for any help,
Ben

Re: [Gmod-ajax] Coupling a highlight event region to an external search

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

Funny, when we were discussing this the other day, this is exactly one of
the use cases I was thinking of (in addition to getting a download of the
sequence).

On Wed, Aug 8, 2018 at 10:49 AM, Colin <col...@gm...> wrote:

> The DebugEvents is a good reference for what you might do as it has the
> "globalHighlightChanged" event that you can subscribe to. Creating a small
> plugin is probably a good model for developing this feature too.
>
>
> As far as DebugEvents not being turned on, plugins should generally be
> only declared in one config file, not a mix of different config files (e.g.
> some in trackList.json, some in jbrowse.conf, etc). This is probably the
> reason for you not seeing the DebugEvents being turned on. This bug tracks
> this as an issue https://github.com/GMOD/jbrowse/issues/897
>
> It was also mentioned recently that maybe after highlighting a region
> there should be a context menu to help users with tasks such as "save
> sequence in region" or other types of features (these features to export
> highlighted region already exist, but having a context menu to easily offer
> this after a highlight operation might be helpful :))
>
>
> -Colin
>
> On Wed, Apr 4, 2018 at 5:33 PM Michael Axtell <mj...@ps...> wrote:
>
>> Hello jbrowse folks, thanks for such a great tool!
>>
>> My javascript skills are poor and so forgive a simple question -- I'd
>> love some quick advice or perhaps a code snippet for this.
>>
>> I'd like to have a user-highlighted region trigger a new window for a
>> custom search page. I'd need the event to pass on the highlighted
>> genome coordinates in the url string to the target page. I can see
>> from the config guide that dojo/topic can be used to subscribe to
>> events, but I don't have the skills to implement this without a bit of
>> help. Can anyone make a suggestion on how to edit this in?  i.e. what
>> would a callback look like, and how should it be implemented?
>>
>> Related note: I tried to activate the DebugEvents plugin by adding
>> this to the jbrowse.conf ::
>>
>> [ plugins.DebugEvents ]
>> location = plugins/DebugEvents
>>
>> , but even after doing so, clearing history and cache on my browser, I
>> didn't see any event messages showing up on the console when I
>> navigated and highlighted regions. I have other plugins working and
>> can see their console messages; just nothing from DebugEvents.
>>
>> JBrowse version 1.12.4
>>
>> Thanks!
>>
>> Mike Axtell
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> 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] Jbrowse sub-feature labels

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

Hi Michal,

There are two separate issues here: getting Chado data into JBrowse, and
displaying the data you have in JBrowse.

For the former, I think you are right that biodb-to-json can be configured
to work the same way as the flatfile script; it's just a little more opaque
for most users, so given the choice, most people would opt for using GFF as
the raw source.

Now for the more difficult problem of displaying your features in JBrowse:
the Segments glyph doesn't really know how to deal features where the edges
overlap or basically don't look like a simple parent with multiple
non-overlapping parts (probably of the same type; but I'm not sure that's a
restriction).

It looks like your features look like this:

nested_repeat (parent)
  repeat_fragment (child that always(?) has the same start and stop as the
parent)
  RR_tract
  long_terminal_repeat (one on each end)

That repeat_fragment feature makes life a little difficult.  If you were to
exclude it, I think the other features may display all in one line.  I
don't recall if there is a config option for displaying the labels of
subfeatures, but the solution to that problem is what I was going to
suggest anyway--creating a custom glyph, so you could control different
coloring for different subparts and force the labeling of subparts if you
want to.  It's not terribly hard to create a new glyph by
subclassing/modifying an existing one.

Scott


On Wed, Aug 8, 2018 at 11:58 AM, Michal Červeňanský <
mis...@gm...> wrote:

> Hello,
> thank you for reply. I am happy to attach gff file. This file is than
> loaded to Chado using gmod_bulk_load_gff3.pl. More information can be
> found here http://gmod.org/wiki/Load_GFF_Into_Chado
> I am not sure how to correctly dump all needed information from db. But i
> believe, that i am able to config biodb-to-json same way as
> flatfile-to-json. I tried what you suggested and result (attached image)
> looks promising. However it seems that i can not see subfeatures, just
> parent ones.
> Sorry about not mentioning the biostar post.
>
> Thanks for your help
> Michal Cervenansky
>
> On Wed, 8 Aug 2018 at 16:41, Colin <col...@gm...> wrote:
>
>> Hi there,
>>
>> It would probably help to have some sort of idea of what type of data is
>> being loaded to see what is going on. Generally the easiest way to load
>> data is just from a simple GFF3 with flatfile-to-json.pl instead of
>> biodb. In this way you can just have a GFF with the parent/child
>> relationships specified like gene->mRNA->exon/CDS (both exon and CDS have
>> the mRNA as the parent)
>>
>> Then use
>>
>> flatfile-to-json.pl --gff features.gff --trackLabel Genes --trackType
>> CanvasFeatures
>>
>> If you do need to use biodb-to-json we might need more details on the
>> biodb dataset being used (maybe a small sample data dump and we can help)
>>
>> Just for cross-reference I think this is a biostars post with the same
>> issue  https://www.biostars.org/p/323306/#329722
>>
>> -Colin
>>
>> On Sun, Jun 17, 2018 at 8:59 AM Michal Červeňanský <
>> mis...@gm...> wrote:
>>
>>> Dear JBrowse team,
>>> I am experiencing difficulties with biodb-to-json.pl configuration
>>> file. I would like to use feature - subfeature relationship and using
>>> various glyphs the visualization looks okey, but i am not able to see
>>> labels, or name tags over the sub-features, i would like them to behave
>>> like ordinary features.
>>> If i use only ordinary features they are drawn under each other. I would
>>> like them to be in one row with sub-features of different color.
>>> I would love to have visualization like Volvox CanvasFeatures -
>>> Protein-coding gene, but with named sub-features.
>>> Can you recommend me how to achieve it ? Any tip would be helpful.
>>>
>>> Thanks for your help.
>>>
>>> Regards
>>> Michal Červeňanský.
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>>> _________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> 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] JBrowse cached location/coordinates not working

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

I think a specific thing that would help is knowing your dataset selector
configuration

-Colin

On Wed, Aug 8, 2018, 5:42 PM Vaneet Lotay <van...@uc...> wrote:

> Hello,
>
>
>
> I noticed when I switched between genomes using the dataset selector that
> it doesn’t come back to the same location or the same gene I was looking
> at, it goes to a different chromosome and different coordinates all
> together.  I’ve seen this issue no matter which genome I go to the second
> time around, the only thing that’s always the same is that it’s always in a
> viewing window that’s zoomed out to a significant amount and appears to be
> always the same Chromosome and coordinates (not the ones I was viewing
> previously).
>
>
>
> I can send you links to my instance directly if you want to see the issue
> I’m talking about.  This is version JBrowse 1.14.2-dev.  I’ve tried it both
> in Chrome and Firefox, same issue.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary AB T2N 1N4*
>
> *CANADA*
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse cached location/coordinates not working

[Vaneet L. <van...@uc...>]

Hello,

I noticed when I switched between genomes using the dataset selector that it doesn't come back to the same location or the same gene I was looking at, it goes to a different chromosome and different coordinates all together.  I've seen this issue no matter which genome I go to the second time around, the only thing that's always the same is that it's always in a viewing window that's zoomed out to a significant amount and appears to be always the same Chromosome and coordinates (not the ones I was viewing previously).

I can send you links to my instance directly if you want to see the issue I'm talking about.  This is version JBrowse 1.14.2-dev.  I've tried it both in Chrome and Firefox, same issue.

Thanks,

Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

Re: [Gmod-ajax] Gene search coordinates issue

[Vaneet L. <van...@uc...>]

Hey Colin,

I had to revert back to JBrowse 1.14.2-dev for now as we needed a stable version of JBrowse for an upcoming conference.  I see that a new version 1.15.1 has been released.  Will try that after the conference and if the issue is still persisting I’ll give you a link to a sample instance so you can see what’s going on.

Thanks,

Vaneet


Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

From: Colin [mailto:col...@gm...]
Sent: Wednesday, August 08, 2018 8:34 AM
To: Vaneet Lotay <van...@uc...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] Gene search coordinates issue

Hi Vaneet, Any update on this?

-Colin

On Wed, Aug 1, 2018 at 10:41 AM Colin <col...@gm...<mailto:col...@gm...>> wrote:
Hi Vaneet,

I'm wondering how to reproduce the issue because I am not able to reproduce it by, for example, switching between the volvox and modENCODE sample browsers.

I guess it might be helpful to see a sample instance that you are using or get a minimal reproducible case!

-Colin

On Mon, Jul 30, 2018 at 2:51 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I’m testing to upgrade to the latest JBrowse release 1.15.0-dev, and I noticed a peculiar issue. I ran the generate-names.pl<http://generate-names.pl> script to generate name indexes for a specific set of my tracks for a given genome.  The gene search works correctly.  I noticed though that when I search for a particular gene, in this case ‘hhex’ in Xenopus tropicalis 9.1 and go to the gene, it retrieves the correct coordinates which are the following:

Chr07:17287891..17303653 (15.76 Kb)

Then if I go to another genome using the dataset selector, then come back to this tropicalis 9.1 genome, it should show the last gene I was looking at but it pops up with an error message box:

Not found: Chr07:17287891..1730365315.76 Kb

This issue happens with any gene searched on any genome as long as I follow the steps I outlined above by searching a gene and then flipping back and forth to the genome version again.  If you look carefully at the error message box (in yellow) it appears it’s missing the space between the end coordinate and the size of the displayed window in parentheses compared to the original coordinates it found in the original search.  Perhaps in the code the space and parentheses are not being put in, or perhaps it should be omitting the window size altogether as it’s not needed to find the gene.

Is this a problem on my end, or is it a bug?

Thanks,

Vaneet



Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

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Re: [Gmod-ajax] Jbrowse sub-feature labels

[Michal Č. <mis...@gm...>]

Hello,
thank you for reply. I am happy to attach gff file. This file is than
loaded to Chado using gmod_bulk_load_gff3.pl. More information can be found
here http://gmod.org/wiki/Load_GFF_Into_Chado
I am not sure how to correctly dump all needed information from db. But i
believe, that i am able to config biodb-to-json same way as
flatfile-to-json. I tried what you suggested and result (attached image)
looks promising. However it seems that i can not see subfeatures, just
parent ones.
Sorry about not mentioning the biostar post.

Thanks for your help
Michal Cervenansky

On Wed, 8 Aug 2018 at 16:41, Colin <col...@gm...> wrote:

> Hi there,
>
> It would probably help to have some sort of idea of what type of data is
> being loaded to see what is going on. Generally the easiest way to load
> data is just from a simple GFF3 with flatfile-to-json.pl instead of
> biodb. In this way you can just have a GFF with the parent/child
> relationships specified like gene->mRNA->exon/CDS (both exon and CDS have
> the mRNA as the parent)
>
> Then use
>
> flatfile-to-json.pl --gff features.gff --trackLabel Genes --trackType
> CanvasFeatures
>
> If you do need to use biodb-to-json we might need more details on the
> biodb dataset being used (maybe a small sample data dump and we can help)
>
> Just for cross-reference I think this is a biostars post with the same
> issue  https://www.biostars.org/p/323306/#329722
>
> -Colin
>
> On Sun, Jun 17, 2018 at 8:59 AM Michal Červeňanský <
> mis...@gm...> wrote:
>
>> Dear JBrowse team,
>> I am experiencing difficulties with biodb-to-json.pl configuration file.
>> I would like to use feature - subfeature relationship and using various
>> glyphs the visualization looks okey, but i am not able to see labels, or
>> name tags over the sub-features, i would like them to behave like ordinary
>> features.
>> If i use only ordinary features they are drawn under each other. I would
>> like them to be in one row with sub-features of different color.
>> I would love to have visualization like Volvox CanvasFeatures -
>> Protein-coding gene, but with named sub-features.
>> Can you recommend me how to achieve it ? Any tip would be helpful.
>>
>> Thanks for your help.
>>
>> Regards
>> Michal Červeňanský.
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] Coupling a highlight event region to an external search

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

The DebugEvents is a good reference for what you might do as it has the
"globalHighlightChanged" event that you can subscribe to. Creating a small
plugin is probably a good model for developing this feature too.


As far as DebugEvents not being turned on, plugins should generally be only
declared in one config file, not a mix of different config files (e.g. some
in trackList.json, some in jbrowse.conf, etc). This is probably the reason
for you not seeing the DebugEvents being turned on. This bug tracks this as
an issue https://github.com/GMOD/jbrowse/issues/897

It was also mentioned recently that maybe after highlighting a region there
should be a context menu to help users with tasks such as "save sequence in
region" or other types of features (these features to export highlighted
region already exist, but having a context menu to easily offer this after
a highlight operation might be helpful :))


-Colin

On Wed, Apr 4, 2018 at 5:33 PM Michael Axtell <mj...@ps...> wrote:

> Hello jbrowse folks, thanks for such a great tool!
>
> My javascript skills are poor and so forgive a simple question -- I'd
> love some quick advice or perhaps a code snippet for this.
>
> I'd like to have a user-highlighted region trigger a new window for a
> custom search page. I'd need the event to pass on the highlighted
> genome coordinates in the url string to the target page. I can see
> from the config guide that dojo/topic can be used to subscribe to
> events, but I don't have the skills to implement this without a bit of
> help. Can anyone make a suggestion on how to edit this in?  i.e. what
> would a callback look like, and how should it be implemented?
>
> Related note: I tried to activate the DebugEvents plugin by adding
> this to the jbrowse.conf ::
>
> [ plugins.DebugEvents ]
> location = plugins/DebugEvents
>
> , but even after doing so, clearing history and cache on my browser, I
> didn't see any event messages showing up on the console when I
> navigated and highlighted regions. I have other plugins working and
> can see their console messages; just nothing from DebugEvents.
>
> JBrowse version 1.12.4
>
> Thanks!
>
> Mike Axtell
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Jbrowse sub-feature labels

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

Hi there,

It would probably help to have some sort of idea of what type of data is
being loaded to see what is going on. Generally the easiest way to load
data is just from a simple GFF3 with flatfile-to-json.pl instead of biodb.
In this way you can just have a GFF with the parent/child relationships
specified like gene->mRNA->exon/CDS (both exon and CDS have the mRNA as the
parent)

Then use

flatfile-to-json.pl --gff features.gff --trackLabel Genes --trackType
CanvasFeatures

If you do need to use biodb-to-json we might need more details on the biodb
dataset being used (maybe a small sample data dump and we can help)

Just for cross-reference I think this is a biostars post with the same
issue  https://www.biostars.org/p/323306/#329722

-Colin

On Sun, Jun 17, 2018 at 8:59 AM Michal Červeňanský <
mis...@gm...> wrote:

> Dear JBrowse team,
> I am experiencing difficulties with biodb-to-json.pl configuration file.
> I would like to use feature - subfeature relationship and using various
> glyphs the visualization looks okey, but i am not able to see labels, or
> name tags over the sub-features, i would like them to behave like ordinary
> features.
> If i use only ordinary features they are drawn under each other. I would
> like them to be in one row with sub-features of different color.
> I would love to have visualization like Volvox CanvasFeatures -
> Protein-coding gene, but with named sub-features.
> Can you recommend me how to achieve it ? Any tip would be helpful.
>
> Thanks for your help.
>
> Regards
> Michal Červeňanský.
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Gene search coordinates issue

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

Hi Vaneet, Any update on this?

-Colin

On Wed, Aug 1, 2018 at 10:41 AM Colin <col...@gm...> wrote:

> Hi Vaneet,
>
> I'm wondering how to reproduce the issue because I am not able to
> reproduce it by, for example, switching between the volvox and modENCODE
> sample browsers.
>
> I guess it might be helpful to see a sample instance that you are using or
> get a minimal reproducible case!
>
> -Colin
>
> On Mon, Jul 30, 2018 at 2:51 PM Vaneet Lotay <van...@uc...>
> wrote:
>
>> Hello,
>>
>>
>>
>> I’m testing to upgrade to the latest JBrowse release 1.15.0-dev, and I
>> noticed a peculiar issue. I ran the generate-names.pl script to generate
>> name indexes for a specific set of my tracks for a given genome.  The gene
>> search works correctly.  I noticed though that when I search for a
>> particular gene, in this case ‘hhex’ in Xenopus tropicalis 9.1 and go to
>> the gene, it retrieves the correct coordinates which are the following:
>>
>>
>>
>> Chr07:17287891..17303653 (15.76 Kb)
>>
>>
>>
>> Then if I go to another genome using the dataset selector, then come back
>> to this tropicalis 9.1 genome, it should show the last gene I was looking
>> at but it pops up with an error message box:
>>
>>
>>
>> Not found: Chr07:17287891..1730365315.76 Kb
>>
>>
>>
>> This issue happens with any gene searched on any genome as long as I
>> follow the steps I outlined above by searching a gene and then flipping
>> back and forth to the genome version again.  If you look carefully at the
>> error message box (in yellow) it appears it’s missing the space between the
>> end coordinate and the size of the displayed window in parentheses compared
>> to the original coordinates it found in the original search.  Perhaps in
>> the code the space and parentheses are not being put in, or perhaps it
>> should be omitting the window size altogether as it’s not needed to find
>> the gene.
>>
>>
>>
>> Is this a problem on my end, or is it a bug?
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Vaneet
>>
>>
>>
>>
>>
>> *Vaneet Lotay*
>>
>> *Xenbase Bioinformatician*
>>
>> *716 ICT Building - University of Calgary*
>>
>> *2500 University Drive NW*
>>
>> *Calgary AB T2N 1N4*
>>
>> *CANADA*
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] insert config on flatfile-to-json.pl command line

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

There is actually a separate argument for flatfile-to-json called
--clientConfig specifically for inserting style configs, so just add

   flatfile-to-json.pl --config '{"category":"$tclas/$assotp"}'
--clientConfig '{"color": "#6fafef"}'

-Colin

On Wed, Aug 8, 2018 at 10:08 AM Zhiliang Hu <hu...@an...> wrote:

> I tried to insert a configuration line on flatfile-to-json.pl command
> line. This (other parts on the command omitted):
>
>    flatfile-to-json.pl --config '{"category":"$tclas/$assotp"}'
>
> works fine; However, this:
>
>    flatfile-to-json.pl --config '{"category":"$tclas/$assotp", \
>              "style":{"color":"#6fafef"}}'
>
> simply got the "style/color" part ignored (no error; not show).
>
> Could someone advice (correct way to do)?
>
> Zhiliang
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] insert config on flatfile-to-json.pl command line

[Zhiliang Hu <hu...@an...>]

I tried to insert a configuration line on flatfile-to-json.pl command 
line. This (other parts on the command omitted):

   flatfile-to-json.pl --config '{"category":"$tclas/$assotp"}'

works fine; However, this:

   flatfile-to-json.pl --config '{"category":"$tclas/$assotp", \
             "style":{"color":"#6fafef"}}'

simply got the "style/color" part ignored (no error; not show).

Could someone advice (correct way to do)?

Zhiliang

Re: [Gmod-ajax] About character encoding of JBrowse and Apollo

[Monica P. <mpo...@gm...>]

Sounds good, thanks!

On Mon, Aug 6, 2018 at 7:41 AM Colin <col...@gm...> wrote:

> If there are any more concerns about encoding feel free to open up github
> issue :)
>
> I didn't mean to be dismissive of encoding concerns but I just wanted to
> explain maybe what is possible with utf8 and ascii.
>
> -Colin
>
> On Thu, Aug 2, 2018 at 2:36 PM Nathan Dunn <nat...@lb...> wrote:
>
>>
>> Grails (in Apollo) can be set to other encodings than UTF-8, but I would
>> agree with Colin that if you can run it through a converter at the end, it
>> would be better.
>>
>> Nathan
>>
>>
>>
>> On Aug 2, 2018, at 11:30 AM, Colin <col...@gm...> wrote:
>>
>> I am hoping to avoid too much complication because I think choosing
>> encoding sounds too crazy but note that UTF8 is the same as ascii for plain
>> English text. This makes UTF8 by far the simplest encoding and it's very
>> widespread now
>>
>> If something needs to be strictly ascii you might do a best effort
>> conversion e.g.
>> https://unix.stackexchange.com/questions/171832/converting-a-utf-8-file-to-ascii-best-effort
>>
>> -Colin
>>
>> On Thu, Aug 2, 2018, 12:53 PM Monica Poelchau <mpo...@gm...>
>> wrote:
>>
>>> Chiming in here - note that we've had trouble submitting Apollo-derived
>>> UTF-8 characters to NCBI, since their genbank gff3 submission portal seems
>>> to only accept ascii (see
>>> https://www.ncbi.nlm.nih.gov/genbank/eukaryotic_genome_submission_annotation/).
>>> It might be nice to have an option to restrict/choose the character
>>> encoding type.
>>>
>>> On Thu, Aug 2, 2018 at 10:31 AM Nathan Dunn <nat...@lb...> wrote:
>>>
>>>>
>>>> Are these the annotated GFF3s from Apollo?
>>>>
>>>> By default the Apollo server is also UTF-8.
>>>>
>>>> However, the database could be set to something entirely different.
>>>>
>>>> Nathan
>>>>
>>>>
>>>> On Aug 2, 2018, at 9:27 AM, 蕭毅 <hsi...@gm...> wrote:
>>>>
>>>> Hi Colin:
>>>>
>>>> Thank you for reply.
>>>> The reason why I asked this is because I get an issue that some of the
>>>> gff3 files retrieved from our apollo/jbrowse instances can't be interpreted
>>>> encoding as utf-8. It turns out I need to interpret it through latin-1
>>>> encoding. I am not an expert of encoding and I am not sure where it comes
>>>> from. That's why I want to know if it's possibly coming from the annotation
>>>> process through apollo/jbrowse.
>>>>
>>>> Thanks.
>>>>
>>>> Best regards,
>>>> Leo (Yi Hsiao)
>>>>
>>>>
>>>>
>>>> Colin <col...@gm...> 於 2018年8月2日 週四 下午12:13寫道：
>>>>
>>>>> I am sorry but I'd like to ask : why are you wondering about encodings
>>>>> specifically?
>>>>>
>>>>> We could talk a lot about encodings but if there's no specific
>>>>> concern, can just assume UTF8 for everything, inputs and outputs, because
>>>>> it is very widely used and accepted and a very simple encoding (there's no
>>>>> byte order marks, its 8 bit compatible, etc.)
>>>>>
>>>>>
>>>>> -Colin
>>>>>
>>>>> On Thu, Aug 2, 2018 at 11:40 AM 蕭毅 <hsi...@gm...> wrote:
>>>>>
>>>>>> Hi Colin:
>>>>>>
>>>>>> I think my question are that
>>>>>> 1. what kind of encoding of character will be put into files when
>>>>>> user adding new annotation ?
>>>>>> 2. How JBrowse/Apollo determine the encoding of the file ? Or it
>>>>>> actually doesn't determine that ? Will it corrupted the GFF files ?
>>>>>> 3. Do we have an option to configure this like all input/output gff3
>>>>>> files will be stored in specific encoding ?
>>>>>>
>>>>>> Best regards,
>>>>>> Leo (Yi Hsiao)
>>>>>>
>>>>>> Colin <col...@gm...> 於 2018年8月2日 週四 上午11:11寫道：
>>>>>>
>>>>>>> I believe utf8 is fine, there is some sample data for JBrowse that
>>>>>>> tests Japanese character set:
>>>>>>>
>>>>>>> See
>>>>>>> http://jbrowse.org/code/JBrowse-1.15.1/?loc=ctgB%3A4615..4865&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2CExampleFeatures%2CEST&data=sample_data%2Fjson%2Fvolvox&highlight=&tracklist=1&highres=2&nav=1&overview=1
>>>>>>>
>>>>>>> If there were any particular concerns about it not working feel free
>>>>>>> to open a github issue!
>>>>>>>
>>>>>>> -Colin
>>>>>>>
>>>>>>> On Thu, Aug 2, 2018 at 9:49 AM 蕭毅 <hsi...@gm...> wrote:
>>>>>>>
>>>>>>>> Hi all:
>>>>>>>>
>>>>>>>> I am curious about the character encoding of JBrowse and Apollo.
>>>>>>>> Is there any requirement for gff3 files ? Like utf-8 or latin-1 ?
>>>>>>>> In gff3 file specification
>>>>>>>> https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md,
>>>>>>>> it recommend usage of Latin-1 or Unicode.
>>>>>>>> I didn't find any information in any documentation. I probably
>>>>>>>> missed it, though.
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>> Leo (Yi Hsiao)
>>>>>>>> --
>>>>>>>> Leo (Yi Hsiao),
>>>>>>>> Bioinformatics Internship,
>>>>>>>> i5k workspace, National Agricultural Library,
>>>>>>>> MD, USA
>>>>>>>>
>>>>>>>> Personal Website: https://hsiaoyi0504.github.io/
>>>>>>>> GitHub: https://github.com/hsiaoyi0504/
>>>>>>>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>>>> engaging tech sites, Slashdot.org <http://slashdot.org/>!
>>>>>>>> http://sdm.link/slashdot
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-ajax mailing list
>>>>>>>> Gmo...@li...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>>>
>>>>>>> --
>>>>>> Leo (Yi Hsiao),
>>>>>> Bioinformatics Internship,
>>>>>> i5k workspace, National Agricultural Library,
>>>>>> MD, USA
>>>>>>
>>>>>> Personal Website: https://hsiaoyi0504.github.io/
>>>>>> GitHub: https://github.com/hsiaoyi0504/
>>>>>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>>>>>
>>>>>> --
>>>> Leo (Yi Hsiao),
>>>> Bioinformatics Internship,
>>>> i5k workspace, National Agricultural Library,
>>>> MD, USA
>>>>
>>>> Personal Website: https://hsiaoyi0504.github.io/
>>>> GitHub: https://github.com/hsiaoyi0504/
>>>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org <http://slashdot.org/>!
>>>> http://sdm.link/slashdot_______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>

Re: [Gmod-ajax] About character encoding of JBrowse and Apollo

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

If there are any more concerns about encoding feel free to open up github
issue :)

I didn't mean to be dismissive of encoding concerns but I just wanted to
explain maybe what is possible with utf8 and ascii.

-Colin

On Thu, Aug 2, 2018 at 2:36 PM Nathan Dunn <nat...@lb...> wrote:

>
> Grails (in Apollo) can be set to other encodings than UTF-8, but I would
> agree with Colin that if you can run it through a converter at the end, it
> would be better.
>
> Nathan
>
>
>
> On Aug 2, 2018, at 11:30 AM, Colin <col...@gm...> wrote:
>
> I am hoping to avoid too much complication because I think choosing
> encoding sounds too crazy but note that UTF8 is the same as ascii for plain
> English text. This makes UTF8 by far the simplest encoding and it's very
> widespread now
>
> If something needs to be strictly ascii you might do a best effort
> conversion e.g.
> https://unix.stackexchange.com/questions/171832/converting-a-utf-8-file-to-ascii-best-effort
>
> -Colin
>
> On Thu, Aug 2, 2018, 12:53 PM Monica Poelchau <mpo...@gm...> wrote:
>
>> Chiming in here - note that we've had trouble submitting Apollo-derived
>> UTF-8 characters to NCBI, since their genbank gff3 submission portal seems
>> to only accept ascii (see
>> https://www.ncbi.nlm.nih.gov/genbank/eukaryotic_genome_submission_annotation/).
>> It might be nice to have an option to restrict/choose the character
>> encoding type.
>>
>> On Thu, Aug 2, 2018 at 10:31 AM Nathan Dunn <nat...@lb...> wrote:
>>
>>>
>>> Are these the annotated GFF3s from Apollo?
>>>
>>> By default the Apollo server is also UTF-8.
>>>
>>> However, the database could be set to something entirely different.
>>>
>>> Nathan
>>>
>>>
>>> On Aug 2, 2018, at 9:27 AM, 蕭毅 <hsi...@gm...> wrote:
>>>
>>> Hi Colin:
>>>
>>> Thank you for reply.
>>> The reason why I asked this is because I get an issue that some of the
>>> gff3 files retrieved from our apollo/jbrowse instances can't be interpreted
>>> encoding as utf-8. It turns out I need to interpret it through latin-1
>>> encoding. I am not an expert of encoding and I am not sure where it comes
>>> from. That's why I want to know if it's possibly coming from the annotation
>>> process through apollo/jbrowse.
>>>
>>> Thanks.
>>>
>>> Best regards,
>>> Leo (Yi Hsiao)
>>>
>>>
>>>
>>> Colin <col...@gm...> 於 2018年8月2日 週四 下午12:13寫道：
>>>
>>>> I am sorry but I'd like to ask : why are you wondering about encodings
>>>> specifically?
>>>>
>>>> We could talk a lot about encodings but if there's no specific concern,
>>>> can just assume UTF8 for everything, inputs and outputs, because it is very
>>>> widely used and accepted and a very simple encoding (there's no byte order
>>>> marks, its 8 bit compatible, etc.)
>>>>
>>>>
>>>> -Colin
>>>>
>>>> On Thu, Aug 2, 2018 at 11:40 AM 蕭毅 <hsi...@gm...> wrote:
>>>>
>>>>> Hi Colin:
>>>>>
>>>>> I think my question are that
>>>>> 1. what kind of encoding of character will be put into files when user
>>>>> adding new annotation ?
>>>>> 2. How JBrowse/Apollo determine the encoding of the file ? Or it
>>>>> actually doesn't determine that ? Will it corrupted the GFF files ?
>>>>> 3. Do we have an option to configure this like all input/output gff3
>>>>> files will be stored in specific encoding ?
>>>>>
>>>>> Best regards,
>>>>> Leo (Yi Hsiao)
>>>>>
>>>>> Colin <col...@gm...> 於 2018年8月2日 週四 上午11:11寫道：
>>>>>
>>>>>> I believe utf8 is fine, there is some sample data for JBrowse that
>>>>>> tests Japanese character set:
>>>>>>
>>>>>> See
>>>>>> http://jbrowse.org/code/JBrowse-1.15.1/?loc=ctgB%3A4615..4865&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2CExampleFeatures%2CEST&data=sample_data%2Fjson%2Fvolvox&highlight=&tracklist=1&highres=2&nav=1&overview=1
>>>>>>
>>>>>> If there were any particular concerns about it not working feel free
>>>>>> to open a github issue!
>>>>>>
>>>>>> -Colin
>>>>>>
>>>>>> On Thu, Aug 2, 2018 at 9:49 AM 蕭毅 <hsi...@gm...> wrote:
>>>>>>
>>>>>>> Hi all:
>>>>>>>
>>>>>>> I am curious about the character encoding of JBrowse and Apollo.
>>>>>>> Is there any requirement for gff3 files ? Like utf-8 or latin-1 ?
>>>>>>> In gff3 file specification
>>>>>>> https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md,
>>>>>>> it recommend usage of Latin-1 or Unicode.
>>>>>>> I didn't find any information in any documentation. I probably
>>>>>>> missed it, though.
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Leo (Yi Hsiao)
>>>>>>> --
>>>>>>> Leo (Yi Hsiao),
>>>>>>> Bioinformatics Internship,
>>>>>>> i5k workspace, National Agricultural Library,
>>>>>>> MD, USA
>>>>>>>
>>>>>>> Personal Website: https://hsiaoyi0504.github.io/
>>>>>>> GitHub: https://github.com/hsiaoyi0504/
>>>>>>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>>> engaging tech sites, Slashdot.org <http://slashdot.org/>!
>>>>>>> http://sdm.link/slashdot
>>>>>>> _______________________________________________
>>>>>>> Gmod-ajax mailing list
>>>>>>> Gmo...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>>
>>>>>> --
>>>>> Leo (Yi Hsiao),
>>>>> Bioinformatics Internship,
>>>>> i5k workspace, National Agricultural Library,
>>>>> MD, USA
>>>>>
>>>>> Personal Website: https://hsiaoyi0504.github.io/
>>>>> GitHub: https://github.com/hsiaoyi0504/
>>>>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>>>>
>>>>> --
>>> Leo (Yi Hsiao),
>>> Bioinformatics Internship,
>>> i5k workspace, National Agricultural Library,
>>> MD, USA
>>>
>>> Personal Website: https://hsiaoyi0504.github.io/
>>> GitHub: https://github.com/hsiaoyi0504/
>>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org <http://slashdot.org/>!
>>> http://sdm.link/slashdot_______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>

Re: [Gmod-ajax] About character encoding of JBrowse and Apollo

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

Grails (in Apollo) can be set to other encodings than UTF-8, but I would agree with Colin that if you can run it through a converter at the end, it would be better. 

Nathan



> On Aug 2, 2018, at 11:30 AM, Colin <col...@gm...> wrote:
> 
> I am hoping to avoid too much complication because I think choosing encoding sounds too crazy but note that UTF8 is the same as ascii for plain English text. This makes UTF8 by far the simplest encoding and it's very widespread now
> 
> If something needs to be strictly ascii you might do a best effort conversion e.g. https://unix.stackexchange.com/questions/171832/converting-a-utf-8-file-to-ascii-best-effort <https://unix.stackexchange.com/questions/171832/converting-a-utf-8-file-to-ascii-best-effort>
> 
> -Colin
> 
> On Thu, Aug 2, 2018, 12:53 PM Monica Poelchau <mpo...@gm... <mailto:mpo...@gm...>> wrote:
> Chiming in here - note that we've had trouble submitting Apollo-derived UTF-8 characters to NCBI, since their genbank gff3 submission portal seems to only accept ascii (see https://www.ncbi.nlm.nih.gov/genbank/eukaryotic_genome_submission_annotation/ <https://www.ncbi.nlm.nih.gov/genbank/eukaryotic_genome_submission_annotation/>). It might be nice to have an option to restrict/choose the character encoding type. 
> 
> On Thu, Aug 2, 2018 at 10:31 AM Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote:
> 
> Are these the annotated GFF3s from Apollo?   
> 
> By default the Apollo server is also UTF-8.  
> 
> However, the database could be set to something entirely different. 
> 
> Nathan
> 
> 
>> On Aug 2, 2018, at 9:27 AM, 蕭毅 <hsi...@gm... <mailto:hsi...@gm...>> wrote:
>> 
>> Hi Colin:
>> 
>> Thank you for reply.
>> The reason why I asked this is because I get an issue that some of the gff3 files retrieved from our apollo/jbrowse instances can't be interpreted encoding as utf-8. It turns out I need to interpret it through latin-1 encoding. I am not an expert of encoding and I am not sure where it comes from. That's why I want to know if it's possibly coming from the annotation process through apollo/jbrowse.
>> 
>> Thanks.
>> 
>> Best regards,
>> Leo (Yi Hsiao)
>> 
>> 
>> 
>> Colin <col...@gm... <mailto:col...@gm...>> 於 2018年8月2日 週四 下午12:13寫道：
>> I am sorry but I'd like to ask : why are you wondering about encodings specifically?
>> 
>> We could talk a lot about encodings but if there's no specific concern, can just assume UTF8 for everything, inputs and outputs, because it is very widely used and accepted and a very simple encoding (there's no byte order marks, its 8 bit compatible, etc.)
>> 
>> 
>> -Colin
>> 
>> On Thu, Aug 2, 2018 at 11:40 AM 蕭毅 <hsi...@gm... <mailto:hsi...@gm...>> wrote:
>> Hi Colin:
>> 
>> I think my question are that 
>> 1. what kind of encoding of character will be put into files when user adding new annotation ?
>> 2. How JBrowse/Apollo determine the encoding of the file ? Or it actually doesn't determine that ? Will it corrupted the GFF files ?
>> 3. Do we have an option to configure this like all input/output gff3 files will be stored in specific encoding ?
>> 
>> Best regards,
>> Leo (Yi Hsiao)
>> 
>> Colin <col...@gm... <mailto:col...@gm...>> 於 2018年8月2日 週四 上午11:11寫道：
>> I believe utf8 is fine, there is some sample data for JBrowse that tests Japanese character set:
>> 
>> See http://jbrowse.org/code/JBrowse-1.15.1/?loc=ctgB%3A4615..4865&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2CExampleFeatures%2CEST&data=sample_data%2Fjson%2Fvolvox&highlight=&tracklist=1&highres=2&nav=1&overview=1 <http://jbrowse.org/code/JBrowse-1.15.1/?loc=ctgB%3A4615..4865&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2CExampleFeatures%2CEST&data=sample_data%2Fjson%2Fvolvox&highlight=&tracklist=1&highres=2&nav=1&overview=1>
>> 
>> If there were any particular concerns about it not working feel free to open a github issue!
>> 
>> -Colin
>> 
>> On Thu, Aug 2, 2018 at 9:49 AM 蕭毅 <hsi...@gm... <mailto:hsi...@gm...>> wrote:
>> Hi all:
>> 
>> I am curious about the character encoding of JBrowse and Apollo.
>> Is there any requirement for gff3 files ? Like utf-8 or latin-1 ?
>> In gff3 file specification https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>, it recommend usage of Latin-1 or Unicode.
>> I didn't find any information in any documentation. I probably missed it, though.
>> 
>> Best regards,
>> Leo (Yi Hsiao)
>> -- 
>> Leo (Yi Hsiao),
>> Bioinformatics Internship,
>> i5k workspace, National Agricultural Library,
>> MD, USA
>> 
>> Personal Website: https://hsiaoyi0504.github.io/ <https://hsiaoyi0504.github.io/>
>> GitHub: https://github.com/hsiaoyi0504/ <https://github.com/hsiaoyi0504/>
>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/ <https://www.linkedin.com/in/hsiaoyi0504/>
>> 
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot <http://sdm.link/slashdot>_______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li... <mailto:Gmo...@li...>
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax>
>> -- 
>> Leo (Yi Hsiao),
>> Bioinformatics Internship,
>> i5k workspace, National Agricultural Library,
>> MD, USA
>> 
>> Personal Website: https://hsiaoyi0504.github.io/ <https://hsiaoyi0504.github.io/>
>> GitHub: https://github.com/hsiaoyi0504/ <https://github.com/hsiaoyi0504/>
>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/ <https://www.linkedin.com/in/hsiaoyi0504/>
>> 
>> -- 
>> Leo (Yi Hsiao),
>> Bioinformatics Internship,
>> i5k workspace, National Agricultural Library,
>> MD, USA
>> 
>> Personal Website: https://hsiaoyi0504.github.io/ <https://hsiaoyi0504.github.io/>
>> GitHub: https://github.com/hsiaoyi0504/ <https://github.com/hsiaoyi0504/>
>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/ <https://www.linkedin.com/in/hsiaoyi0504/>
>> 
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot_______________________________________________ <http://sdm.link/slashdot_______________________________________________>
>> Gmod-ajax mailing list
>> Gmo...@li... <mailto:Gmo...@li...>
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax>
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot <http://sdm.link/slashdot>_______________________________________________
> Gmod-ajax mailing list
> Gmo...@li... <mailto:Gmo...@li...>
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
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> Gmod-ajax mailing list
> Gmo...@li... <mailto:Gmo...@li...>
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax>

Re: [Gmod-ajax] About character encoding of JBrowse and Apollo

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

I am hoping to avoid too much complication because I think choosing
encoding sounds too crazy but note that UTF8 is the same as ascii for plain
English text. This makes UTF8 by far the simplest encoding and it's very
widespread now

If something needs to be strictly ascii you might do a best effort
conversion e.g.
https://unix.stackexchange.com/questions/171832/converting-a-utf-8-file-to-ascii-best-effort

-Colin

On Thu, Aug 2, 2018, 12:53 PM Monica Poelchau <mpo...@gm...> wrote:

> Chiming in here - note that we've had trouble submitting Apollo-derived
> UTF-8 characters to NCBI, since their genbank gff3 submission portal seems
> to only accept ascii (see
> https://www.ncbi.nlm.nih.gov/genbank/eukaryotic_genome_submission_annotation/).
> It might be nice to have an option to restrict/choose the character
> encoding type.
>
> On Thu, Aug 2, 2018 at 10:31 AM Nathan Dunn <nat...@lb...> wrote:
>
>>
>> Are these the annotated GFF3s from Apollo?
>>
>> By default the Apollo server is also UTF-8.
>>
>> However, the database could be set to something entirely different.
>>
>> Nathan
>>
>>
>> On Aug 2, 2018, at 9:27 AM, 蕭毅 <hsi...@gm...> wrote:
>>
>> Hi Colin:
>>
>> Thank you for reply.
>> The reason why I asked this is because I get an issue that some of the
>> gff3 files retrieved from our apollo/jbrowse instances can't be interpreted
>> encoding as utf-8. It turns out I need to interpret it through latin-1
>> encoding. I am not an expert of encoding and I am not sure where it comes
>> from. That's why I want to know if it's possibly coming from the annotation
>> process through apollo/jbrowse.
>>
>> Thanks.
>>
>> Best regards,
>> Leo (Yi Hsiao)
>>
>>
>>
>> Colin <col...@gm...> 於 2018年8月2日 週四 下午12:13寫道：
>>
>>> I am sorry but I'd like to ask : why are you wondering about encodings
>>> specifically?
>>>
>>> We could talk a lot about encodings but if there's no specific concern,
>>> can just assume UTF8 for everything, inputs and outputs, because it is very
>>> widely used and accepted and a very simple encoding (there's no byte order
>>> marks, its 8 bit compatible, etc.)
>>>
>>>
>>> -Colin
>>>
>>> On Thu, Aug 2, 2018 at 11:40 AM 蕭毅 <hsi...@gm...> wrote:
>>>
>>>> Hi Colin:
>>>>
>>>> I think my question are that
>>>> 1. what kind of encoding of character will be put into files when user
>>>> adding new annotation ?
>>>> 2. How JBrowse/Apollo determine the encoding of the file ? Or it
>>>> actually doesn't determine that ? Will it corrupted the GFF files ?
>>>> 3. Do we have an option to configure this like all input/output gff3
>>>> files will be stored in specific encoding ?
>>>>
>>>> Best regards,
>>>> Leo (Yi Hsiao)
>>>>
>>>> Colin <col...@gm...> 於 2018年8月2日 週四 上午11:11寫道：
>>>>
>>>>> I believe utf8 is fine, there is some sample data for JBrowse that
>>>>> tests Japanese character set:
>>>>>
>>>>> See
>>>>> http://jbrowse.org/code/JBrowse-1.15.1/?loc=ctgB%3A4615..4865&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2CExampleFeatures%2CEST&data=sample_data%2Fjson%2Fvolvox&highlight=&tracklist=1&highres=2&nav=1&overview=1
>>>>>
>>>>> If there were any particular concerns about it not working feel free
>>>>> to open a github issue!
>>>>>
>>>>> -Colin
>>>>>
>>>>> On Thu, Aug 2, 2018 at 9:49 AM 蕭毅 <hsi...@gm...> wrote:
>>>>>
>>>>>> Hi all:
>>>>>>
>>>>>> I am curious about the character encoding of JBrowse and Apollo.
>>>>>> Is there any requirement for gff3 files ? Like utf-8 or latin-1 ?
>>>>>> In gff3 file specification
>>>>>> https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md,
>>>>>> it recommend usage of Latin-1 or Unicode.
>>>>>> I didn't find any information in any documentation. I probably missed
>>>>>> it, though.
>>>>>>
>>>>>> Best regards,
>>>>>> Leo (Yi Hsiao)
>>>>>> --
>>>>>> Leo (Yi Hsiao),
>>>>>> Bioinformatics Internship,
>>>>>> i5k workspace, National Agricultural Library,
>>>>>> MD, USA
>>>>>>
>>>>>> Personal Website: https://hsiaoyi0504.github.io/
>>>>>> GitHub: https://github.com/hsiaoyi0504/
>>>>>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>> _______________________________________________
>>>>>> Gmod-ajax mailing list
>>>>>> Gmo...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>
>>>>> --
>>>> Leo (Yi Hsiao),
>>>> Bioinformatics Internship,
>>>> i5k workspace, National Agricultural Library,
>>>> MD, USA
>>>>
>>>> Personal Website: https://hsiaoyi0504.github.io/
>>>> GitHub: https://github.com/hsiaoyi0504/
>>>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>>>
>>>> --
>> Leo (Yi Hsiao),
>> Bioinformatics Internship,
>> i5k workspace, National Agricultural Library,
>> MD, USA
>>
>> Personal Website: https://hsiaoyi0504.github.io/
>> GitHub: https://github.com/hsiaoyi0504/
>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org!
>> http://sdm.link/slashdot_______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] About character encoding of JBrowse and Apollo

[Monica P. <mpo...@gm...>]

Chiming in here - note that we've had trouble submitting Apollo-derived
UTF-8 characters to NCBI, since their genbank gff3 submission portal seems
to only accept ascii (see
https://www.ncbi.nlm.nih.gov/genbank/eukaryotic_genome_submission_annotation/).
It might be nice to have an option to restrict/choose the character
encoding type.

On Thu, Aug 2, 2018 at 10:31 AM Nathan Dunn <nat...@lb...> wrote:

>
> Are these the annotated GFF3s from Apollo?
>
> By default the Apollo server is also UTF-8.
>
> However, the database could be set to something entirely different.
>
> Nathan
>
>
> On Aug 2, 2018, at 9:27 AM, 蕭毅 <hsi...@gm...> wrote:
>
> Hi Colin:
>
> Thank you for reply.
> The reason why I asked this is because I get an issue that some of the
> gff3 files retrieved from our apollo/jbrowse instances can't be interpreted
> encoding as utf-8. It turns out I need to interpret it through latin-1
> encoding. I am not an expert of encoding and I am not sure where it comes
> from. That's why I want to know if it's possibly coming from the annotation
> process through apollo/jbrowse.
>
> Thanks.
>
> Best regards,
> Leo (Yi Hsiao)
>
>
>
> Colin <col...@gm...> 於 2018年8月2日 週四 下午12:13寫道：
>
>> I am sorry but I'd like to ask : why are you wondering about encodings
>> specifically?
>>
>> We could talk a lot about encodings but if there's no specific concern,
>> can just assume UTF8 for everything, inputs and outputs, because it is very
>> widely used and accepted and a very simple encoding (there's no byte order
>> marks, its 8 bit compatible, etc.)
>>
>>
>> -Colin
>>
>> On Thu, Aug 2, 2018 at 11:40 AM 蕭毅 <hsi...@gm...> wrote:
>>
>>> Hi Colin:
>>>
>>> I think my question are that
>>> 1. what kind of encoding of character will be put into files when user
>>> adding new annotation ?
>>> 2. How JBrowse/Apollo determine the encoding of the file ? Or it
>>> actually doesn't determine that ? Will it corrupted the GFF files ?
>>> 3. Do we have an option to configure this like all input/output gff3
>>> files will be stored in specific encoding ?
>>>
>>> Best regards,
>>> Leo (Yi Hsiao)
>>>
>>> Colin <col...@gm...> 於 2018年8月2日 週四 上午11:11寫道：
>>>
>>>> I believe utf8 is fine, there is some sample data for JBrowse that
>>>> tests Japanese character set:
>>>>
>>>> See
>>>> http://jbrowse.org/code/JBrowse-1.15.1/?loc=ctgB%3A4615..4865&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2CExampleFeatures%2CEST&data=sample_data%2Fjson%2Fvolvox&highlight=&tracklist=1&highres=2&nav=1&overview=1
>>>>
>>>> If there were any particular concerns about it not working feel free to
>>>> open a github issue!
>>>>
>>>> -Colin
>>>>
>>>> On Thu, Aug 2, 2018 at 9:49 AM 蕭毅 <hsi...@gm...> wrote:
>>>>
>>>>> Hi all:
>>>>>
>>>>> I am curious about the character encoding of JBrowse and Apollo.
>>>>> Is there any requirement for gff3 files ? Like utf-8 or latin-1 ?
>>>>> In gff3 file specification
>>>>> https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md,
>>>>> it recommend usage of Latin-1 or Unicode.
>>>>> I didn't find any information in any documentation. I probably missed
>>>>> it, though.
>>>>>
>>>>> Best regards,
>>>>> Leo (Yi Hsiao)
>>>>> --
>>>>> Leo (Yi Hsiao),
>>>>> Bioinformatics Internship,
>>>>> i5k workspace, National Agricultural Library,
>>>>> MD, USA
>>>>>
>>>>> Personal Website: https://hsiaoyi0504.github.io/
>>>>> GitHub: https://github.com/hsiaoyi0504/
>>>>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Check out the vibrant tech community on one of the world's most
>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> Gmo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>
>>>> --
>>> Leo (Yi Hsiao),
>>> Bioinformatics Internship,
>>> i5k workspace, National Agricultural Library,
>>> MD, USA
>>>
>>> Personal Website: https://hsiaoyi0504.github.io/
>>> GitHub: https://github.com/hsiaoyi0504/
>>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>>
>>> --
> Leo (Yi Hsiao),
> Bioinformatics Internship,
> i5k workspace, National Agricultural Library,
> MD, USA
>
> Personal Website: https://hsiaoyi0504.github.io/
> GitHub: https://github.com/hsiaoyi0504/
> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org!
> http://sdm.link/slashdot_______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] About character encoding of JBrowse and Apollo

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

Are these the annotated GFF3s from Apollo?   

By default the Apollo server is also UTF-8.  

However, the database could be set to something entirely different. 

Nathan


> On Aug 2, 2018, at 9:27 AM, 蕭毅 <hsi...@gm...> wrote:
> 
> Hi Colin:
> 
> Thank you for reply.
> The reason why I asked this is because I get an issue that some of the gff3 files retrieved from our apollo/jbrowse instances can't be interpreted encoding as utf-8. It turns out I need to interpret it through latin-1 encoding. I am not an expert of encoding and I am not sure where it comes from. That's why I want to know if it's possibly coming from the annotation process through apollo/jbrowse.
> 
> Thanks.
> 
> Best regards,
> Leo (Yi Hsiao)
> 
> 
> 
> Colin <col...@gm... <mailto:col...@gm...>> 於 2018年8月2日 週四 下午12:13寫道：
> I am sorry but I'd like to ask : why are you wondering about encodings specifically?
> 
> We could talk a lot about encodings but if there's no specific concern, can just assume UTF8 for everything, inputs and outputs, because it is very widely used and accepted and a very simple encoding (there's no byte order marks, its 8 bit compatible, etc.)
> 
> 
> -Colin
> 
> On Thu, Aug 2, 2018 at 11:40 AM 蕭毅 <hsi...@gm... <mailto:hsi...@gm...>> wrote:
> Hi Colin:
> 
> I think my question are that 
> 1. what kind of encoding of character will be put into files when user adding new annotation ?
> 2. How JBrowse/Apollo determine the encoding of the file ? Or it actually doesn't determine that ? Will it corrupted the GFF files ?
> 3. Do we have an option to configure this like all input/output gff3 files will be stored in specific encoding ?
> 
> Best regards,
> Leo (Yi Hsiao)
> 
> Colin <col...@gm... <mailto:col...@gm...>> 於 2018年8月2日 週四 上午11:11寫道：
> I believe utf8 is fine, there is some sample data for JBrowse that tests Japanese character set:
> 
> See http://jbrowse.org/code/JBrowse-1.15.1/?loc=ctgB%3A4615..4865&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2CExampleFeatures%2CEST&data=sample_data%2Fjson%2Fvolvox&highlight=&tracklist=1&highres=2&nav=1&overview=1 <http://jbrowse.org/code/JBrowse-1.15.1/?loc=ctgB%3A4615..4865&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2CExampleFeatures%2CEST&data=sample_data%2Fjson%2Fvolvox&highlight=&tracklist=1&highres=2&nav=1&overview=1>
> 
> If there were any particular concerns about it not working feel free to open a github issue!
> 
> -Colin
> 
> On Thu, Aug 2, 2018 at 9:49 AM 蕭毅 <hsi...@gm... <mailto:hsi...@gm...>> wrote:
> Hi all:
> 
> I am curious about the character encoding of JBrowse and Apollo.
> Is there any requirement for gff3 files ? Like utf-8 or latin-1 ?
> In gff3 file specification https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>, it recommend usage of Latin-1 or Unicode.
> I didn't find any information in any documentation. I probably missed it, though.
> 
> Best regards,
> Leo (Yi Hsiao)
> -- 
> Leo (Yi Hsiao),
> Bioinformatics Internship,
> i5k workspace, National Agricultural Library,
> MD, USA
> 
> Personal Website: https://hsiaoyi0504.github.io/ <https://hsiaoyi0504.github.io/>
> GitHub: https://github.com/hsiaoyi0504/ <https://github.com/hsiaoyi0504/>
> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/ <https://www.linkedin.com/in/hsiaoyi0504/>
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot <http://sdm.link/slashdot>_______________________________________________
> Gmod-ajax mailing list
> Gmo...@li... <mailto:Gmo...@li...>
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax>
> -- 
> Leo (Yi Hsiao),
> Bioinformatics Internship,
> i5k workspace, National Agricultural Library,
> MD, USA
> 
> Personal Website: https://hsiaoyi0504.github.io/ <https://hsiaoyi0504.github.io/>
> GitHub: https://github.com/hsiaoyi0504/ <https://github.com/hsiaoyi0504/>
> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/ <https://www.linkedin.com/in/hsiaoyi0504/>
> 
> -- 
> Leo (Yi Hsiao),
> Bioinformatics Internship,
> i5k workspace, National Agricultural Library,
> MD, USA
> 
> Personal Website: https://hsiaoyi0504.github.io/ <https://hsiaoyi0504.github.io/>
> GitHub: https://github.com/hsiaoyi0504/ <https://github.com/hsiaoyi0504/>
> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/ <https://www.linkedin.com/in/hsiaoyi0504/>
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] About character encoding of JBrowse and Apollo

[蕭毅 <hsi...@gm...>]

Hi Colin:

Thank you for reply.
The reason why I asked this is because I get an issue that some of the gff3
files retrieved from our apollo/jbrowse instances can't be interpreted
encoding as utf-8. It turns out I need to interpret it through latin-1
encoding. I am not an expert of encoding and I am not sure where it comes
from. That's why I want to know if it's possibly coming from the annotation
process through apollo/jbrowse.

Thanks.

Best regards,
Leo (Yi Hsiao)



Colin <col...@gm...> 於 2018年8月2日 週四 下午12:13寫道：

> I am sorry but I'd like to ask : why are you wondering about encodings
> specifically?
>
> We could talk a lot about encodings but if there's no specific concern,
> can just assume UTF8 for everything, inputs and outputs, because it is very
> widely used and accepted and a very simple encoding (there's no byte order
> marks, its 8 bit compatible, etc.)
>
>
> -Colin
>
> On Thu, Aug 2, 2018 at 11:40 AM 蕭毅 <hsi...@gm...> wrote:
>
>> Hi Colin:
>>
>> I think my question are that
>> 1. what kind of encoding of character will be put into files when user
>> adding new annotation ?
>> 2. How JBrowse/Apollo determine the encoding of the file ? Or it actually
>> doesn't determine that ? Will it corrupted the GFF files ?
>> 3. Do we have an option to configure this like all input/output gff3
>> files will be stored in specific encoding ?
>>
>> Best regards,
>> Leo (Yi Hsiao)
>>
>> Colin <col...@gm...> 於 2018年8月2日 週四 上午11:11寫道：
>>
>>> I believe utf8 is fine, there is some sample data for JBrowse that tests
>>> Japanese character set:
>>>
>>> See
>>> http://jbrowse.org/code/JBrowse-1.15.1/?loc=ctgB%3A4615..4865&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2CExampleFeatures%2CEST&data=sample_data%2Fjson%2Fvolvox&highlight=&tracklist=1&highres=2&nav=1&overview=1
>>>
>>> If there were any particular concerns about it not working feel free to
>>> open a github issue!
>>>
>>> -Colin
>>>
>>> On Thu, Aug 2, 2018 at 9:49 AM 蕭毅 <hsi...@gm...> wrote:
>>>
>>>> Hi all:
>>>>
>>>> I am curious about the character encoding of JBrowse and Apollo.
>>>> Is there any requirement for gff3 files ? Like utf-8 or latin-1 ?
>>>> In gff3 file specification
>>>> https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md,
>>>> it recommend usage of Latin-1 or Unicode.
>>>> I didn't find any information in any documentation. I probably missed
>>>> it, though.
>>>>
>>>> Best regards,
>>>> Leo (Yi Hsiao)
>>>> --
>>>> Leo (Yi Hsiao),
>>>> Bioinformatics Internship,
>>>> i5k workspace, National Agricultural Library,
>>>> MD, USA
>>>>
>>>> Personal Website: https://hsiaoyi0504.github.io/
>>>> GitHub: https://github.com/hsiaoyi0504/
>>>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>> --
>> Leo (Yi Hsiao),
>> Bioinformatics Internship,
>> i5k workspace, National Agricultural Library,
>> MD, USA
>>
>> Personal Website: https://hsiaoyi0504.github.io/
>> GitHub: https://github.com/hsiaoyi0504/
>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>
>> --
Leo (Yi Hsiao),
Bioinformatics Internship,
i5k workspace, National Agricultural Library,
MD, USA

Personal Website: https://hsiaoyi0504.github.io/
GitHub: https://github.com/hsiaoyi0504/
LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/

Re: [Gmod-ajax] About character encoding of JBrowse and Apollo

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

I am sorry but I'd like to ask : why are you wondering about encodings
specifically?

We could talk a lot about encodings but if there's no specific concern, can
just assume UTF8 for everything, inputs and outputs, because it is very
widely used and accepted and a very simple encoding (there's no byte order
marks, its 8 bit compatible, etc.)


-Colin

On Thu, Aug 2, 2018 at 11:40 AM 蕭毅 <hsi...@gm...> wrote:

> Hi Colin:
>
> I think my question are that
> 1. what kind of encoding of character will be put into files when user
> adding new annotation ?
> 2. How JBrowse/Apollo determine the encoding of the file ? Or it actually
> doesn't determine that ? Will it corrupted the GFF files ?
> 3. Do we have an option to configure this like all input/output gff3 files
> will be stored in specific encoding ?
>
> Best regards,
> Leo (Yi Hsiao)
>
> Colin <col...@gm...> 於 2018年8月2日 週四 上午11:11寫道：
>
>> I believe utf8 is fine, there is some sample data for JBrowse that tests
>> Japanese character set:
>>
>> See
>> http://jbrowse.org/code/JBrowse-1.15.1/?loc=ctgB%3A4615..4865&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2CExampleFeatures%2CEST&data=sample_data%2Fjson%2Fvolvox&highlight=&tracklist=1&highres=2&nav=1&overview=1
>>
>> If there were any particular concerns about it not working feel free to
>> open a github issue!
>>
>> -Colin
>>
>> On Thu, Aug 2, 2018 at 9:49 AM 蕭毅 <hsi...@gm...> wrote:
>>
>>> Hi all:
>>>
>>> I am curious about the character encoding of JBrowse and Apollo.
>>> Is there any requirement for gff3 files ? Like utf-8 or latin-1 ?
>>> In gff3 file specification
>>> https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md,
>>> it recommend usage of Latin-1 or Unicode.
>>> I didn't find any information in any documentation. I probably missed
>>> it, though.
>>>
>>> Best regards,
>>> Leo (Yi Hsiao)
>>> --
>>> Leo (Yi Hsiao),
>>> Bioinformatics Internship,
>>> i5k workspace, National Agricultural Library,
>>> MD, USA
>>>
>>> Personal Website: https://hsiaoyi0504.github.io/
>>> GitHub: https://github.com/hsiaoyi0504/
>>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>> --
> Leo (Yi Hsiao),
> Bioinformatics Internship,
> i5k workspace, National Agricultural Library,
> MD, USA
>
> Personal Website: https://hsiaoyi0504.github.io/
> GitHub: https://github.com/hsiaoyi0504/
> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>
>

Re: [Gmod-ajax] About character encoding of JBrowse and Apollo

[蕭毅 <hsi...@gm...>]

Hi Colin:

I think my question are that
1. what kind of encoding of character will be put into files when user
adding new annotation ?
2. How JBrowse/Apollo determine the encoding of the file ? Or it actually
doesn't determine that ? Will it corrupted the GFF files ?
3. Do we have an option to configure this like all input/output gff3 files
will be stored in specific encoding ?

Best regards,
Leo (Yi Hsiao)

Colin <col...@gm...> 於 2018年8月2日 週四 上午11:11寫道：

> I believe utf8 is fine, there is some sample data for JBrowse that tests
> Japanese character set:
>
> See
> http://jbrowse.org/code/JBrowse-1.15.1/?loc=ctgB%3A4615..4865&tracks=DNA%2CTranscript%2Cvolvox_microarray_bw_density%2Cvolvox_microarray_bw_xyplot%2CExampleFeatures%2CEST&data=sample_data%2Fjson%2Fvolvox&highlight=&tracklist=1&highres=2&nav=1&overview=1
>
> If there were any particular concerns about it not working feel free to
> open a github issue!
>
> -Colin
>
> On Thu, Aug 2, 2018 at 9:49 AM 蕭毅 <hsi...@gm...> wrote:
>
>> Hi all:
>>
>> I am curious about the character encoding of JBrowse and Apollo.
>> Is there any requirement for gff3 files ? Like utf-8 or latin-1 ?
>> In gff3 file specification
>> https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md,
>> it recommend usage of Latin-1 or Unicode.
>> I didn't find any information in any documentation. I probably missed it,
>> though.
>>
>> Best regards,
>> Leo (Yi Hsiao)
>> --
>> Leo (Yi Hsiao),
>> Bioinformatics Internship,
>> i5k workspace, National Agricultural Library,
>> MD, USA
>>
>> Personal Website: https://hsiaoyi0504.github.io/
>> GitHub: https://github.com/hsiaoyi0504/
>> LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
> --
Leo (Yi Hsiao),
Bioinformatics Internship,
i5k workspace, National Agricultural Library,
MD, USA

Personal Website: https://hsiaoyi0504.github.io/
GitHub: https://github.com/hsiaoyi0504/
LinkedIn: https://www.linkedin.com/in/hsiaoyi0504/