gmod-ajax

[Gmod-ajax] How to remove a track

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Hi all,
  Can anyone tell me how to delete a track completely in JBrowse?
  I tried to delete the track directory (eg. TrackToBeDelete) in the
path of jbrowse/data/tracks/RefSeq/ TrackToBeDelete. However, in the
jbrowse the track name is still there, only the actual data is not
displaying. It seems to me that the track information is recorded in the
browserRoot level instead of the dataRoot level, doesn't it? How can I
remove a track completely? Thanks in advance.

Regards,
Kenneth

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[Gmod-ajax] using biodb-to-json.pl on volvox_conf.json but no track was outputted

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Hello all,
  I downloaded the VMware ('Ending Image' in
http://gmod.org/wiki/JBrowse_Tutorial) and tried to convert the
configuration file (volvox_conf.json) to json. However no track was
outputted by the following steps:
- go to '/var/www/jbrowse/docs/tutorial/conf_files'
- change the db_args attribute to point to the correct data directory:
"-dir": "/var/www/jbrowse/docs/tutorial/data_files" },
- in the same conf_files directory and type:
../../../bin/biodb-to-json.pl --conf volvox.json
- it created directories 'data/tracks', but somehow nothing is in both
dir or sub-dir.

Did I do anything wrong or missed out any crucial steps? (I was
expecting the biodb-to-json.pl will generate all tracks in the config
file directly.)
Thanks.

Regards,
Kenneth

---------------------------------------------------------------------------------------------------------
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Re: [Gmod-ajax] using biodb-to-json.pl on volvox_conf.json but no track was outputted

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

Did you run prepare-refseqs.pl?

Also, I think that vmware image has git installed, so it might help to 
go into
/var/www/jbrowse/
and run "git pull" to update that jbrowse installation.

Also, by default, the "data" directory is created as a subdirectory of 
the working directory that the scripts are run from, and (by default) 
the index.html file expects the "data" directory to be in the same 
directory as the index.html file.  So if you run the scripts from the 
"jbrowse" directory (i.e., if you run them like: bin/prepare-refseqs.pl) 
then you can just use the defaults, otherwise use the --out parameter to 
specify the location of the data directory.

Hope this helps,
Mitch

On 03/17/2010 09:26 AM, CHAN, KENNETH 1 [AG/7721] wrote:
> Hello all,
>    I downloaded the VMware ('Ending Image' in
> http://gmod.org/wiki/JBrowse_Tutorial) and tried to convert the
> configuration file (volvox_conf.json) to json. However no track was
> outputted by the following steps:
> - go to '/var/www/jbrowse/docs/tutorial/conf_files'
> - change the db_args attribute to point to the correct data directory:
> "-dir": "/var/www/jbrowse/docs/tutorial/data_files" },
> - in the same conf_files directory and type:
> ../../../bin/biodb-to-json.pl --conf volvox.json
> - it created directories 'data/tracks', but somehow nothing is in both
> dir or sub-dir.
>
> Did I do anything wrong or missed out any crucial steps? (I was
> expecting the biodb-to-json.pl will generate all tracks in the config
> file directly.)
> Thanks.
>
> Regards,
> Kenneth
>
> ---------------------------------------------------------------------------------------------------------
> This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.
>
>
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> ---------------------------------------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------------
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Re: [Gmod-ajax] using biodb-to-json.pl on volvox_conf.json but no track was outputted

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Thanks Mitch for the detailed reply.
  Previously I thought biodb-to-json.pl will automatically treat the
first line in volvox.gff3 (ctgA example ........ Name=ctgA) as the
reference sequence similar to gbrowse so no prepare-refseqs.pl is
required when directly converting the config file. Anyway, I was wrong. 
 Just tried the 'git pull', but showed 'Failed to find a valid git
directory'. That's not important anyway.
 For other users' reference, after I used prepare-refseqs.pl and
biodb-to-json.pl. Since I used the --out parameter to specify a new
output location, I needed to manually modify the index.html file so that
it points to the correct location of refSeqs.js and trackInfo.js.

  Thank the whole jbrowse developing team for developing such a nice UI.
Hope it will continue to be successful and provide richer features and
functionalities in the soon future.

Regards,
Kenneth



-----Original Message-----
From: Mitch Skinner [mailto:mit...@be...] 
Sent: Thursday, March 18, 2010 2:48 AM
To: CHAN, KENNETH 1 [AG/7721]
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] using biodb-to-json.pl on volvox_conf.json but
no track was outputted

Did you run prepare-refseqs.pl?

Also, I think that vmware image has git installed, so it might help to 
go into
/var/www/jbrowse/
and run "git pull" to update that jbrowse installation.

Also, by default, the "data" directory is created as a subdirectory of 
the working directory that the scripts are run from, and (by default) 
the index.html file expects the "data" directory to be in the same 
directory as the index.html file.  So if you run the scripts from the 
"jbrowse" directory (i.e., if you run them like: bin/prepare-refseqs.pl)

then you can just use the defaults, otherwise use the --out parameter to

specify the location of the data directory.

Hope this helps,
Mitch

On 03/17/2010 09:26 AM, CHAN, KENNETH 1 [AG/7721] wrote:
> Hello all,
>    I downloaded the VMware ('Ending Image' in
> http://gmod.org/wiki/JBrowse_Tutorial) and tried to convert the
> configuration file (volvox_conf.json) to json. However no track was
> outputted by the following steps:
> - go to '/var/www/jbrowse/docs/tutorial/conf_files'
> - change the db_args attribute to point to the correct data directory:
> "-dir": "/var/www/jbrowse/docs/tutorial/data_files" },
> - in the same conf_files directory and type:
> ../../../bin/biodb-to-json.pl --conf volvox.json
> - it created directories 'data/tracks', but somehow nothing is in both
> dir or sub-dir.
>
> Did I do anything wrong or missed out any crucial steps? (I was
> expecting the biodb-to-json.pl will generate all tracks in the config
> file directly.)
> Thanks.
>
> Regards,
> Kenneth
>
>
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---------------------------------
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please notify the sender immediately. Please delete it and all
attachments from any servers, hard drives or any other media. Other use
of this e-mail by you is strictly prohibited.
>
>
> All e-mails and attachments sent and received are subject to
monitoring, reading and archival by Monsanto, including its
subsidiaries. The recipient of this e-mail is solely responsible for
checking for the presence of "Viruses" or other "Malware". Monsanto,
along with its subsidiaries, accepts no liability for any damage caused
by any such code transmitted by or accompanying this e-mail or any
attachment.
>
------------------------------------------------------------------------
---------------------------------
>
>
>
------------------------------------------------------------------------
------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
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>    



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[Gmod-ajax] wig-to-json.pl gives low resolution image and the values didn't correspond to the values in wig file

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Hi guys,
  I encountered a strange result when using wig-to-json.pl. The
quantitative track I got has a very low resolution and the values
doesn't seem like corresponding to the wiggle file.
  I attached the wiggle file and the resulted picture after applied the
following command:

./bin/wig-to-json.pl --wig
/bifx/apache/htdocs/gbrowse2/databases/te_viewer/testing/TS_76715_CG_R_C
overage.wig --out "event_data/TS_76715/" --key "Reads Coverage" --tile
"event_data/TS_76715/" --tracklabel Coverage

  I noticed that the above command didn't generate the 'tiles' directory
in the "event_data/TS_76715" as I specified. If I took out the tile bit
(--tile "even_data/TS_76715"). The tile directory appears in the data
dir. I tried to copy the tile dir to the "event_data/TS_76715" manually
but the resolution didn't change. May I ask what the generated "tiles"
directory is for? And do you have any idea how I can fix this problem of
low resolution. Thanks.

Regards,
Kenneth

---------------------------------------------------------------------------------------------------------
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Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and the values didn't correspond to the values in wig file

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

CHAN, KENNETH 1 [AG/7721] wrote:
> Hi guys,
>   I encountered a strange result when using wig-to-json.pl. The
> quantitative track I got has a very low resolution and the values
> doesn't seem like corresponding to the wiggle file.

Hi, I haven't gotten a chance to reproduce this or look at it in detail 
yet, but I do have a quick answer to part of this:

Currently, JBrowse renders wiggle files up to one pixel per base 
(because that's the highest possible data density) and then uses the web 
browser to stretch the images when the user is zoomed in closer than one 
pixel per base.  On large genomes, this saves a lot of disk space and 
processing time compared to rendering images at higher resolutions.  
Plus, JBrowse allows for variable font sizes, so at the highest zoom 
level, different users will have different values for the number of 
pixels per base.  So even if we wanted to generate higher resolution 
images, we wouldn't be able to pick a scale factor for the highest zoom 
level that would work exactly for everyone; in many cases the web 
browser would still have to stretch or shrink the image.

Originally, the web browsers all used a scaling algorithm that kept the 
results crisp-looking, but more recently they've started to use a 
smoother (bicubic) scaling algorithm by default, and wiggle tracks 
started looking fuzzy in JBrowse when they're zoomed in all the way.

The web browsers have just started implementing switches that will allow 
us to specify the old scaling method:
https://developer.mozilla.org/en/CSS/image-rendering

and writing the JBrowse code to set that value appropriately is on our 
to-do list (although if anyone wants to tackle it, that would be 
welcome; it should be simple to set the relevant CSS styles on the 
images in ImageTrack.js).

Mitch

Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and the values didn't correspond to the values in wig file

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

Mitch Skinner wrote:
> Currently, JBrowse renders wiggle files up to one pixel per base

I meant to say:

JBrowse renders wiggle files *at zoom levels* up to one pixel per base

Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and the values didn't correspond to the values in wig file

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Thanks Mitch, I found out that the low resolution problem does not
happen in internet explorer (I used IE 6). But it occurs in google
Chrome and Firefox.
  The most problematic thing is not the resolution issue but the empty
regions (the white vertical lines among the green bar that can be seen
in the attachment) in the graph. I have manually checked the wig file.
There should not be any empty regions. Would it be the problem in my
data or a problem in wig-to-json.pl? Again, this is the command I used:

./bin/wig-to-json.pl --wig
/bifx/apache/htdocs/gbrowse2/databases/te_viewer/testing/TS_76715_CG_R_C
overage.wig --out "event_data/TS_76715/" --key "Reads Coverage" --tile
"event_data/TS_76715/" --tracklabel Coverage


Regards,
Kenneth



-----Original Message-----
From: Mitch Skinner [mailto:mit...@be...] 
Sent: Saturday, March 20, 2010 9:55 AM
To: CHAN, KENNETH 1 [AG/7721]
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and
the values didn't correspond to the values in wig file

CHAN, KENNETH 1 [AG/7721] wrote:
> Hi guys,
>   I encountered a strange result when using wig-to-json.pl. The
> quantitative track I got has a very low resolution and the values
> doesn't seem like corresponding to the wiggle file.

Hi, I haven't gotten a chance to reproduce this or look at it in detail 
yet, but I do have a quick answer to part of this:

Currently, JBrowse renders wiggle files up to one pixel per base 
(because that's the highest possible data density) and then uses the web

browser to stretch the images when the user is zoomed in closer than one

pixel per base.  On large genomes, this saves a lot of disk space and 
processing time compared to rendering images at higher resolutions.  
Plus, JBrowse allows for variable font sizes, so at the highest zoom 
level, different users will have different values for the number of 
pixels per base.  So even if we wanted to generate higher resolution 
images, we wouldn't be able to pick a scale factor for the highest zoom 
level that would work exactly for everyone; in many cases the web 
browser would still have to stretch or shrink the image.

Originally, the web browsers all used a scaling algorithm that kept the 
results crisp-looking, but more recently they've started to use a 
smoother (bicubic) scaling algorithm by default, and wiggle tracks 
started looking fuzzy in JBrowse when they're zoomed in all the way.

The web browsers have just started implementing switches that will allow

us to specify the old scaling method:
https://developer.mozilla.org/en/CSS/image-rendering

and writing the JBrowse code to set that value appropriately is on our 
to-do list (although if anyone wants to tackle it, that would be 
welcome; it should be simple to set the relevant CSS styles on the 
images in ImageTrack.js).

Mitch


---------------------------------------------------------------------------------------------------------
This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.


All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.
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Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and the values didn't correspond to the values in wig file

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

Hi, I'm sorry it's taken so long for me to get back to you.

This file is in the wiggle "bed" format, which UCSC now calls the 
"bedgraph" format.  That particular format (and not the other wiggle 
forms) is defined to use zero-based, half-open coordinates:
http://genome.ucsc.edu/goldenPath/help/bedgraph.html

In other words, these lines in the file:

chr10   0       1       4
chr10   2       3       5

specify that there's a value of 4 at base 0, no data at base 1, and a 
value of 5 at base 2.  The "no data" at base 1 is what is giving you 
those blank spaces.

Just add 1 to the stop positions in your data, and the blank spaces will 
get filled in.  I attached a version of your original file where I've 
done this in order to show exactly what I mean.

Regards,
Mitch

CHAN, KENNETH 1 [AG/7721] wrote:
> Thanks Mitch, I found out that the low resolution problem does not
> happen in internet explorer (I used IE 6). But it occurs in google
> Chrome and Firefox.
>   The most problematic thing is not the resolution issue but the empty
> regions (the white vertical lines among the green bar that can be seen
> in the attachment) in the graph. I have manually checked the wig file.
> There should not be any empty regions. Would it be the problem in my
> data or a problem in wig-to-json.pl? Again, this is the command I used:
>
> ./bin/wig-to-json.pl --wig
> /bifx/apache/htdocs/gbrowse2/databases/te_viewer/testing/TS_76715_CG_R_C
> overage.wig --out "event_data/TS_76715/" --key "Reads Coverage" --tile
> "event_data/TS_76715/" --tracklabel Coverage
>
>
> Regards,
> Kenneth
>   

Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and the values didn't correspond to the values in wig file

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Hello Mitch,
  Got it!! This is very helpful to correct my data display. Thanks a
lot!!

Regards,
Kenneth



> -----Original Message-----
> From: Mitch Skinner [mailto:mit...@be...]
> Sent: Saturday, April 24, 2010 12:13 PM
> To: CHAN, KENNETH 1 [AG/7721]
> Cc: gmo...@li...
> Subject: Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and
the
> values didn't correspond to the values in wig file
> 
> Hi, I'm sorry it's taken so long for me to get back to you.
> 
> This file is in the wiggle "bed" format, which UCSC now calls the
"bedgraph"
> format.  That particular format (and not the other wiggle
> forms) is defined to use zero-based, half-open coordinates:
> http://genome.ucsc.edu/goldenPath/help/bedgraph.html
> 
> In other words, these lines in the file:
> 
> chr10   0       1       4
> chr10   2       3       5
> 
> specify that there's a value of 4 at base 0, no data at base 1, and a
value of
> 5 at base 2.  The "no data" at base 1 is what is giving you those
blank spaces.
> 
> Just add 1 to the stop positions in your data, and the blank spaces
will get
> filled in.  I attached a version of your original file where I've done
this in
> order to show exactly what I mean.
> 
> Regards,
> Mitch
> 
> CHAN, KENNETH 1 [AG/7721] wrote:
> > Thanks Mitch, I found out that the low resolution problem does not
> > happen in internet explorer (I used IE 6). But it occurs in google
> > Chrome and Firefox.
> >   The most problematic thing is not the resolution issue but the
empty
> > regions (the white vertical lines among the green bar that can be
seen
> > in the attachment) in the graph. I have manually checked the wig
file.
> > There should not be any empty regions. Would it be the problem in my
> > data or a problem in wig-to-json.pl? Again, this is the command I
used:
> >
> > ./bin/wig-to-json.pl --wig
> >
/bifx/apache/htdocs/gbrowse2/databases/te_viewer/testing/TS_76715_CG_R
> > _C overage.wig --out "event_data/TS_76715/" --key "Reads Coverage"
> > --tile "event_data/TS_76715/" --tracklabel Coverage
> >
> >
> > Regards,
> > Kenneth
> >


---------------------------------------------------------------------------------------------------------
This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.


All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.
---------------------------------------------------------------------------------------------------------

Re: [Gmod-ajax] How to remove a track

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

Hi Kenneth,

Currently the easiest way to do this is to edit the file 
data/trackInfo.js (where 'data' is your dataRoot directory). Within this 
file you will see one clause like the following for each track:

    {
       "url" : "data/tracks/{refseq}/sts_markers/trackData.json",
       "type" : "FeatureTrack",
       "label" : "sts_markers",
       "key" : "STS Markers"
    },

Just delete that clause and the track will disappear. We do clearly need 
  a script to do this, and I've added a request ticket for that.

best, Ian


CHAN, KENNETH 1 [AG/7721] wrote:
> Hi all,
>   Can anyone tell me how to delete a track completely in JBrowse?
>   I tried to delete the track directory (eg. TrackToBeDelete) in the
> path of jbrowse/data/tracks/RefSeq/ TrackToBeDelete. However, in the
> jbrowse the track name is still there, only the actual data is not
> displaying. It seems to me that the track information is recorded in the
> browserRoot level instead of the dataRoot level, doesn't it? How can I
> remove a track completely? Thanks in advance.
> 
> Regards,
> Kenneth
> 
> ---------------------------------------------------------------------------------------------------------
> This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.
> 
> 
> All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.
> ---------------------------------------------------------------------------------------------------------
> 
> 
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Gmod-ajax mailing list
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