shalabh sharma | 1 Nov 16:09 2008
Picon

Re: mysql database for gbrowse

Hey Dave,
                  Thanks for reply. Actually what i was doing, i have different gff file for different chromosome and i was just combining them all and loading it.
But ya know the problem is solved. I loaded all the files (for different chromosomes) together on single command line.

Thanks
Shalabh


On Fri, Oct 31, 2008 at 5:15 PM, Dave Clements, GMOD Help Desk <gmodhelp-gM/Ye1E23mwN+BqQ9rBEUg@public.gmane.org> wrote:
Shalabh,

More than one chromosome per GFF file and MySQL database should be
fine.  Does each of the chomosomes have a full-length entry for it in
the GFF file?  For example:

chrI    SGD     chromosome      1       230208  .       .       .       ID=chrI;dbxref=NCBI:NC_001133
chrI ...
chrII   SGD     chromosome      1       813178  .       .       .       ID=chrII;dbxref=NCBI:NC_001134
chrII ...

Dave C.


On Fri, Oct 31, 2008 at 7:23 AM, shalabh sharma
<shalabh.sharma7-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
> Hi,
> I am using gbrowse V1.7 om MacOX (Tiger).
> I am building a database on mysql . I have one (.gff3) file for all the
> chromosomes (chr1-chr21).
> I have loaded that file in mysql database, it worked fine.
> But the problem is that when i type any other chromosome other then chr1
> (like chr7 or chr21) it says :
>
> The landmark named chr7 is not recognized. See the help pages for
> suggestions
>
> but its working fine for chr1.
> Is it that i have to make different mysql database for different
> chromosomes?
> I would really appreciate if anyone can help me out.
>
> Thanks
> Shalabh
>
>
>
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Lincoln Stein | 1 Nov 19:29 2008
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Re: Version of Bio::Perl required by Gbrowse 1.69?

I have fixed the problem with #html fragments. The latest tarball (as of November 1) should correct the problem.

Where can I get a copy of the VistaPlot plugin? I would like to figure out what aspect of FeatureFile broke it.

Lincoln

On Wed, Oct 29, 2008 at 9:15 PM, Shengqiang Shu <sqshu-/3juihCSby0@public.gmane.org> wrote:
Hi, Scott and everyone.

I have a problem with installed gbrowse released 1.69 (tarball from sourceforge) and bioperlive nightly build tarball (Oct. 29 2008). Installation is fine.

There are couple of issues:

1) I can not have '#' in a html element for a tag like header in gbrowse config file. It failed to slurp in the text after first '#' for header value. For now I remove parts with '#' (it was for style of span element).

2) I had a prereleased 1.69 stable version working. This time it worked fine for everything except one plugin (VistaPlot) which added a track of multiple xy plots. The current version drew only black bars instead of xy plots (please see attached the screen shots from the same data). Now if I swapped out bioperl-live modules with bioperl 1.52 ones, it worked fine. We do want to move forward with released 1.69 with the correct version of bioperl.

VistaPlot plugin was developed by somebody else. Basically, in annotate method, it creates Bio::Graphics::FeatureFile object, then for each plot, it uses att_type method to add an xyplot glyph and add_feature method to add the underling feature for the plot to the object, and at end returns the object. I noticed Bio::Graphics::FeatureFile has changed a lot. I am not sure it has any thing to do with my problem. Any pointer would be greatly appreciated.

Thanks.

Shu







On Aug 26, 2008, at 11:11 AM, Scott Cain wrote:

Hi Aaron,

No, unfortunately, BioPerl 1.5.2 is too old, even though it is the
most recent release.  You need a nightly snapshot or svn checkout of
bioperl-live.  You can get the nightly snapshot either by running the
gbrowse net installer or by downloading it from bioperl.org:

 http://www.bioperl.org/DIST/nightly_builds/

Scott


On Tue, Aug 26, 2008 at 1:52 PM, Aaron Gussman <agussman-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
What is the version of BioPerl required by Gbrowse 1.69?

I attempted to install Gbrowse and received the following message:
perl Makefile.PL APACHE=/export/prog/apache
...
Installed Bio::Graphics version 1.654 is less than desired version 1.7.
You need to update your BioPerl installation to greater than version 1.5.2.

Died at Makefile.PL line 266, <DATA> line 192.

I guess that means I need to upgrade the full Bio::Perl to the 1.5.2,
Developer Release (I think this is the link:
http://www.bioperl.org/wiki/Getting_BioPerl#Bioperl_1.5.2.2C_Developer_Release)?

Thanks,
Aaron

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Lincoln Stein | 1 Nov 19:49 2008
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Re: Version of Bio::Perl required by Gbrowse 1.69?

Hi,

Actually, I think I know what was broken. In the new FeatureFile, the add_feature() method no longer honors the feature type if it is passed in the method call, but only uses the feature's primary tag. This is a rather deep problem because FeatureFile no longer stores the feature itself, but instead uses a variety of underlying databases, so I've worked around the problem by having add_feature() change the feature's primary_tag to the provided type.

Could you try the 1 November bioperl tarball and see if the VistaPlot starts working again?

Lincoln

On Wed, Oct 29, 2008 at 9:15 PM, Shengqiang Shu <sqshu-/3juihCSby0@public.gmane.org> wrote:
Hi, Scott and everyone.

I have a problem with installed gbrowse released 1.69 (tarball from sourceforge) and bioperlive nightly build tarball (Oct. 29 2008). Installation is fine.

There are couple of issues:

1) I can not have '#' in a html element for a tag like header in gbrowse config file. It failed to slurp in the text after first '#' for header value. For now I remove parts with '#' (it was for style of span element).

2) I had a prereleased 1.69 stable version working. This time it worked fine for everything except one plugin (VistaPlot) which added a track of multiple xy plots. The current version drew only black bars instead of xy plots (please see attached the screen shots from the same data). Now if I swapped out bioperl-live modules with bioperl 1.52 ones, it worked fine. We do want to move forward with released 1.69 with the correct version of bioperl.

VistaPlot plugin was developed by somebody else. Basically, in annotate method, it creates Bio::Graphics::FeatureFile object, then for each plot, it uses att_type method to add an xyplot glyph and add_feature method to add the underling feature for the plot to the object, and at end returns the object. I noticed Bio::Graphics::FeatureFile has changed a lot. I am not sure it has any thing to do with my problem. Any pointer would be greatly appreciated.

Thanks.

Shu







On Aug 26, 2008, at 11:11 AM, Scott Cain wrote:

Hi Aaron,

No, unfortunately, BioPerl 1.5.2 is too old, even though it is the
most recent release.  You need a nightly snapshot or svn checkout of
bioperl-live.  You can get the nightly snapshot either by running the
gbrowse net installer or by downloading it from bioperl.org:

 http://www.bioperl.org/DIST/nightly_builds/

Scott


On Tue, Aug 26, 2008 at 1:52 PM, Aaron Gussman <agussman-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
What is the version of BioPerl required by Gbrowse 1.69?

I attempted to install Gbrowse and received the following message:
perl Makefile.PL APACHE=/export/prog/apache
...
Installed Bio::Graphics version 1.654 is less than desired version 1.7.
You need to update your BioPerl installation to greater than version 1.5.2.

Died at Makefile.PL line 266, <DATA> line 192.

I guess that means I need to upgrade the full Bio::Perl to the 1.5.2,
Developer Release (I think this is the link:
http://www.bioperl.org/wiki/Getting_BioPerl#Bioperl_1.5.2.2C_Developer_Release)?

Thanks,
Aaron

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------------------------------------------------------------------------
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Cold Spring Harbor Laboratory

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--
Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Stacey Quinn <Stacey.Quinn-O2sQSXo6EZOw5LPnMra/2Q@public.gmane.org>

Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724 USA
(516) 367-8380
Assistant: Sandra Michelsen <michelse-FePsPjn27tw@public.gmane.org>
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Joan Pontius | 3 Nov 17:28 2008

Re: wiggle questions

Sheldon

Thanks to your email I think I have what I want, things seem to be  
working.

for problem #1, if I understand it, the wiggle format "description="  
tag when converted to
GFF format, ends up being the label, not the description.

for problem #2, that was my fault, I wasn't using unique values for  
name=

for problem #3, now I have new questions about color and color  
intensity display,
is it possible to display color using red/green instead of dark/light.

Thanks in advance

Joan

On Oct 31, 2008, at 1:39 PM, Sheldon McKay wrote:

> Hi Joan,
>
> Assuming you are using local, rather than uploaded wiggle files.
>
>> 1. On the WiggleTracks page->
>> http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
>> In the first example image, the description is to the left of the
>> wiggletrack
>> while further down, it is under the track. How can I designate my
>> preference?
>> Mine are coming up underneath the track and I'd rather have it to  
>> the side.
>
> The label_position in the first example is set to "left" and "top" in
> the later example.
>
> You control this in your config stanza
> [WTRACK]
> glyph = wiggle_density
> label_position = left
>
> For the description, it is usually on the bottom in a blue font.  If
> you want to have description text on the left, you can use a callback
> to add the desired text to the label, then use label_position = left
>
> [WTRACK]
> glyph = wiggle_density
> label_position = left
> label = sub {
>    my $f = shift;
>    my ($desc) = $f->attributes('Note');
>    $desc ||= $f->source_tag;
>    return $desc;
>  }
>
> However, take care that your description is not too long, or it will
> be clipped on the left-hand side.  You also need to set a generous
> image padding in your config (image_padding = xxx) so there is room
> for your left-hand label.
>
> NB: If you are uploading the data, rather than using it locally, you
> can't use the "label=sub{...}" callback.  However, you can edit the
> GFF (the GFF is what you get after you click 'Edit' after uploading a
> WIG file) and add (or edit) a Name=Your+description+text; to each
> line.  That way the label should grab the text by default.
>
>
>> 2. Is there a limit to the number of features I put in a track.
>> Right now, I have 70,000 SNPs each with 150 statistical tests  
>> associated
>> with them.
>> Is this going to crash?
>
> Could you clarify?  You want 150 data points/snp?  Could you send a
> sample of the data?
>
>> I am trying to debug problems, sometimes the wiggle track is  
>> displayed as  a
>> solid band,
>> I wonder if that is a problem with size, or getting timed out  or  
>> something.
>> Should they be cut up into smaller files representing regions of the
>> chromosome?
>
> It would be helpful to have your config info plus some sample data  
> here
>
>> 3. What do the color intensities represent?  Is the scale  
>> determined by max
>> and min of each individual wig file?
>
> Yes.  You can use autoscaling or fix the scale via the max_score and
> min_score options
>
>> Is default (no transformation) a linear scale?
> Yes.
>
>> If I want all tracks to have the same
>> scale, how would I designate that.
>
> use the same max_score and min_score for each track.
>
>
> Sheldon
>
> -- 
> Sheldon J. McKay, PhD
> Research Investigator
> Cold Spring Harbor Laboratory
> Office: 516-367-6998
> Fax: 516 367-6851
> Email: mckays@...
> Skype: mckays630
>

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Alexie Papanicolaou | 3 Nov 19:38 2008

gbrowse unaligned again?

Hello

A while back Lincoln had fixed a bug on gbrowse_img (embed=1) regarding the alignment of the image map and the graphics (map was wee bit higher). I just put the current dev version and the bug is there.

can anyone else see this?

thanks
alexie

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shalabh sharma | 3 Nov 21:15 2008
Picon

converting Promer (Mummer) output files to GFF

Hi All,
            Is there any way we can convert output files from Promer (Mummer) to GFF format?

Thanks
Shalabh

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Sheldon McKay | 3 Nov 20:46 2008
Picon

Re: wiggle questions

Yes, I think this is what you want
pos_color = red
neg_color - green
(or the other way around?)

Sheldon

On Mon, Nov 3, 2008 at 11:28 AM, Joan Pontius <pontiusj@...> wrote:
> Sheldon
>
> Thanks to your email I think I have what I want, things seem to be
> working.
>
> for problem #1, if I understand it, the wiggle format "description="
> tag when converted to
> GFF format, ends up being the label, not the description.
>
> for problem #2, that was my fault, I wasn't using unique values for
> name=
>
> for problem #3, now I have new questions about color and color
> intensity display,
> is it possible to display color using red/green instead of dark/light.
>
>
> Thanks in advance
>
> Joan
>
>
>
>
> On Oct 31, 2008, at 1:39 PM, Sheldon McKay wrote:
>
>> Hi Joan,
>>
>> Assuming you are using local, rather than uploaded wiggle files.
>>
>>> 1. On the WiggleTracks page->
>>> http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
>>> In the first example image, the description is to the left of the
>>> wiggletrack
>>> while further down, it is under the track. How can I designate my
>>> preference?
>>> Mine are coming up underneath the track and I'd rather have it to
>>> the side.
>>
>> The label_position in the first example is set to "left" and "top" in
>> the later example.
>>
>> You control this in your config stanza
>> [WTRACK]
>> glyph = wiggle_density
>> label_position = left
>>
>> For the description, it is usually on the bottom in a blue font.  If
>> you want to have description text on the left, you can use a callback
>> to add the desired text to the label, then use label_position = left
>>
>> [WTRACK]
>> glyph = wiggle_density
>> label_position = left
>> label = sub {
>>    my $f = shift;
>>    my ($desc) = $f->attributes('Note');
>>    $desc ||= $f->source_tag;
>>    return $desc;
>>  }
>>
>> However, take care that your description is not too long, or it will
>> be clipped on the left-hand side.  You also need to set a generous
>> image padding in your config (image_padding = xxx) so there is room
>> for your left-hand label.
>>
>> NB: If you are uploading the data, rather than using it locally, you
>> can't use the "label=sub{...}" callback.  However, you can edit the
>> GFF (the GFF is what you get after you click 'Edit' after uploading a
>> WIG file) and add (or edit) a Name=Your+description+text; to each
>> line.  That way the label should grab the text by default.
>>
>>
>>> 2. Is there a limit to the number of features I put in a track.
>>> Right now, I have 70,000 SNPs each with 150 statistical tests
>>> associated
>>> with them.
>>> Is this going to crash?
>>
>> Could you clarify?  You want 150 data points/snp?  Could you send a
>> sample of the data?
>>
>>> I am trying to debug problems, sometimes the wiggle track is
>>> displayed as  a
>>> solid band,
>>> I wonder if that is a problem with size, or getting timed out  or
>>> something.
>>> Should they be cut up into smaller files representing regions of the
>>> chromosome?
>>
>> It would be helpful to have your config info plus some sample data
>> here
>>
>>> 3. What do the color intensities represent?  Is the scale
>>> determined by max
>>> and min of each individual wig file?
>>
>> Yes.  You can use autoscaling or fix the scale via the max_score and
>> min_score options
>>
>>> Is default (no transformation) a linear scale?
>> Yes.
>>
>>> If I want all tracks to have the same
>>> scale, how would I designate that.
>>
>> use the same max_score and min_score for each track.
>>
>>
>> Sheldon
>>
>> --
>> Sheldon J. McKay, PhD
>> Research Investigator
>> Cold Spring Harbor Laboratory
>> Office: 516-367-6998
>> Fax: 516 367-6851
>> Email: mckays@...
>> Skype: mckays630
>>
>
>
> -------------------------------------------------------------------------
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> Build the coolest Linux based applications with Moblin SDK & win great prizes
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--

-- 
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Research Investigator
Cold Spring Harbor Laboratory
Office: 516-367-6998
Fax: 516 367-6851
Email: mckays@...
Skype: mckays630

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Bakir, Burcu | 3 Nov 21:18 2008
Picon

Filtering search results of GBrowse


Hi,

I would like to learn if there is a way to filter GBrowse search by
attribute type? Like the search only returns a specific type of object
(i.e.gene). May be via changing some settings at config file? I have
checked the following link, but it doesn't answer my question.
http://gmod.org/wiki/GBrowse_Configuration_HOWTO#FILTERING_SEARCH_RESULT
S

Thanks,

Burcu

-----Original Message-----
From: gmod-gbrowse-request@...
[mailto:gmod-gbrowse-request@...] 
Sent: Monday, November 03, 2008 1:28 PM
To: gmod-gbrowse@...
Subject: Gmod-gbrowse Digest, Vol 30, Issue 2

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Today's Topics:

   1. Re: Version of Bio::Perl required by Gbrowse 1.69? (Lincoln Stein)
   2. simple but weird problem (Zhiliang Hu)
   3. Re: wiggle questions (Joan Pontius)
   4. Re: simple but weird problem (Sheldon McKay)

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

Message: 1
Date: Sat, 1 Nov 2008 14:49:46 -0400
From: "Lincoln Stein" <lincoln.stein@...>
Subject: Re: [Gmod-gbrowse] Version of Bio::Perl required by Gbrowse
	1.69?
To: "Shengqiang Shu" <sqshu@...>
Cc: Scott Cain <cain.cshl@...>,
	gmod-gbrowse@...
Message-ID:
	<6dce9a0b0811011149r5d7273bdp8106d54c7f1b76b@...>
Content-Type: text/plain; charset="iso-8859-1"

Hi,

Actually, I think I know what was broken. In the new FeatureFile, the
add_feature() method no longer honors the feature type if it is passed
in
the method call, but only uses the feature's primary tag. This is a
rather
deep problem because FeatureFile no longer stores the feature itself,
but
instead uses a variety of underlying databases, so I've worked around
the
problem by having add_feature() *change* the feature's primary_tag to
the
provided type.

Could you try the 1 November bioperl tarball and see if the VistaPlot
starts
working again?

Lincoln

On Wed, Oct 29, 2008 at 9:15 PM, Shengqiang Shu <sqshu@...> wrote:

> Hi, Scott and everyone.
>
> I have a problem with installed gbrowse released 1.69 (tarball from
> sourceforge) and bioperlive nightly build tarball (Oct. 29 2008).
> Installation is fine.
>
> There are couple of issues:
>
> 1) I can not have '#' in a html element for a tag like header in
gbrowse
> config file. It failed to slurp in the text after first '#' for header
> value. For now I remove parts with '#' (it was for style of span
element).
>
> 2) I had a prereleased 1.69 stable version working. This time it
worked
> fine for everything except one plugin (VistaPlot) which added a track
of
> multiple xy plots. The current version drew only black bars instead of
xy
> plots (please see attached the screen shots from the same data). Now
if I
> swapped out bioperl-live modules with bioperl 1.52 ones, it worked
fine. We
> do want to move forward with released 1.69 with the correct version of
> bioperl.
>
> VistaPlot plugin was developed by somebody else. Basically, in
annotate
> method, it creates Bio::Graphics::FeatureFile object, then for each
plot, it
> uses att_type method to add an xyplot glyph and add_feature method to
add
> the underling feature for the plot to the object, and at end returns
the
> object. I noticed Bio::Graphics::FeatureFile has changed a lot. I am
not
> sure it has any thing to do with my problem. Any pointer would be
greatly
> appreciated.
>
> Thanks.
>
> Shu
>
>
>
>
>
>
>
> On Aug 26, 2008, at 11:11 AM, Scott Cain wrote:
>
>  Hi Aaron,
>>
>> No, unfortunately, BioPerl 1.5.2 is too old, even though it is the
>> most recent release.  You need a nightly snapshot or svn checkout of
>> bioperl-live.  You can get the nightly snapshot either by running the
>> gbrowse net installer or by downloading it from bioperl.org:
>>
>>  http://www.bioperl.org/DIST/nightly_builds/
>>
>> Scott
>>
>>
>> On Tue, Aug 26, 2008 at 1:52 PM, Aaron Gussman <agussman@...>
>> wrote:
>>
>>> What is the version of BioPerl required by Gbrowse 1.69?
>>>
>>> I attempted to install Gbrowse and received the following message:
>>>
>>>> perl Makefile.PL APACHE=/export/prog/apache
>>>>
>>> ...
>>> Installed Bio::Graphics version 1.654 is less than desired version
1.7.
>>> You need to update your BioPerl installation to greater than version
>>> 1.5.2.
>>>
>>> Died at Makefile.PL line 266, <DATA> line 192.
>>>
>>> I guess that means I need to upgrade the full Bio::Perl to the
1.5.2,
>>> Developer Release (I think this is the link:
>>> http://www.bioperl.org/wiki/
>>> Getting_BioPerl#Bioperl_1.5.2.2C_Developer_Release)?
>>>
>>> Thanks,
>>> Aaron
>>>
>>>
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>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
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>>> Build the coolest Linux based applications with Moblin SDK & win
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>>>
>>
>>
>> --
>>
------------------------------------------------------------------------
>> Scott Cain, Ph. D. cain.cshl@...
>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>> Cold Spring Harbor Laboratory
>>
>>
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>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win
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>> prizes
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>> world
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>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
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> challenge
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> prizes
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>

-- 
Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Stacey Quinn <Stacey.Quinn@...>

Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724 USA
(516) 367-8380
Assistant: Sandra Michelsen <michelse@...>
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------------------------------

Message: 2
Date: Mon, 3 Nov 2008 13:08:08 -0600 (CST)
From: Zhiliang Hu <hu@...>
Subject: [Gmod-gbrowse] simple but weird problem
To: Gbrowse Mailing List <gmod-gbrowse@...>
Message-ID:
	<Pine.LNX.4.61.0811031259430.13634@...>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

In a process to get popup balloon out, I found basic html tags fail to 
show up:

balloon tips = 1

### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ###
# inside the <head></head> section
head = <title>Cattle Genome Track</title>
# at the top...
header = <h1>Cattle Genome Track - Chromosome 8 </h1>
footer = <h1>add footer</h1>
#footer = sub {
#               my $file =
"/usr/local/apache/doc/default/trailerb.tmpl";
#               my $tailout;
#               if (-e $file) {
#                 open(FILE, "$file");
#                   while (<FILE>) {
#                     $tailout .= "$_";
#                   }
#                 close(FILE);
#               } else {
#                   $tailout = "<font color=red>Trailerb not
found</font>";
#               }
#               return ($tailout);
#             }
# Various places where you can insert your own HTML -- see configuration
docs
html1 = <h2> html1</h2>
html2 = <h2> Html2</h2>
html3 = <h2> Html3</h2>
html4 = <h2> Html4</h2>
html5 = <h2> Html5</h2>
html6 = <h2> Html6</h2>

I tried to back up by reducing my conf file to see what's going on but
do 
not find clues/lucks.  They stay not shown.  What could be the cause?
(Not the browser/cache problem).

Thanks,
Zhiliang

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

Message: 3
Date: Mon, 3 Nov 2008 11:28:48 -0500
From: Joan Pontius <pontiusj@...>
Subject: Re: [Gmod-gbrowse] wiggle questions
To: Gbrowse Mailing List <gmod-gbrowse@...>
Message-ID: <E95D52DE-03CC-4C85-AFB8-2839E47A7AD1@...>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Sheldon

Thanks to your email I think I have what I want, things seem to be  
working.

for problem #1, if I understand it, the wiggle format "description="  
tag when converted to
GFF format, ends up being the label, not the description.

for problem #2, that was my fault, I wasn't using unique values for  
name=

for problem #3, now I have new questions about color and color  
intensity display,
is it possible to display color using red/green instead of dark/light.

Thanks in advance

Joan

On Oct 31, 2008, at 1:39 PM, Sheldon McKay wrote:

> Hi Joan,
>
> Assuming you are using local, rather than uploaded wiggle files.
>
>> 1. On the WiggleTracks page->
>> http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks
>> In the first example image, the description is to the left of the
>> wiggletrack
>> while further down, it is under the track. How can I designate my
>> preference?
>> Mine are coming up underneath the track and I'd rather have it to  
>> the side.
>
> The label_position in the first example is set to "left" and "top" in
> the later example.
>
> You control this in your config stanza
> [WTRACK]
> glyph = wiggle_density
> label_position = left
>
> For the description, it is usually on the bottom in a blue font.  If
> you want to have description text on the left, you can use a callback
> to add the desired text to the label, then use label_position = left
>
> [WTRACK]
> glyph = wiggle_density
> label_position = left
> label = sub {
>    my $f = shift;
>    my ($desc) = $f->attributes('Note');
>    $desc ||= $f->source_tag;
>    return $desc;
>  }
>
> However, take care that your description is not too long, or it will
> be clipped on the left-hand side.  You also need to set a generous
> image padding in your config (image_padding = xxx) so there is room
> for your left-hand label.
>
> NB: If you are uploading the data, rather than using it locally, you
> can't use the "label=sub{...}" callback.  However, you can edit the
> GFF (the GFF is what you get after you click 'Edit' after uploading a
> WIG file) and add (or edit) a Name=Your+description+text; to each
> line.  That way the label should grab the text by default.
>
>
>> 2. Is there a limit to the number of features I put in a track.
>> Right now, I have 70,000 SNPs each with 150 statistical tests  
>> associated
>> with them.
>> Is this going to crash?
>
> Could you clarify?  You want 150 data points/snp?  Could you send a
> sample of the data?
>
>> I am trying to debug problems, sometimes the wiggle track is  
>> displayed as  a
>> solid band,
>> I wonder if that is a problem with size, or getting timed out  or  
>> something.
>> Should they be cut up into smaller files representing regions of the
>> chromosome?
>
> It would be helpful to have your config info plus some sample data  
> here
>
>> 3. What do the color intensities represent?  Is the scale  
>> determined by max
>> and min of each individual wig file?
>
> Yes.  You can use autoscaling or fix the scale via the max_score and
> min_score options
>
>> Is default (no transformation) a linear scale?
> Yes.
>
>> If I want all tracks to have the same
>> scale, how would I designate that.
>
> use the same max_score and min_score for each track.
>
>
> Sheldon
>
> -- 
> Sheldon J. McKay, PhD
> Research Investigator
> Cold Spring Harbor Laboratory
> Office: 516-367-6998
> Fax: 516 367-6851
> Email: mckays@...
> Skype: mckays630
>

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

Message: 4
Date: Mon, 3 Nov 2008 14:27:59 -0500
From: "Sheldon McKay" <sheldon.mckay@...>
Subject: Re: [Gmod-gbrowse] simple but weird problem
To: "Zhiliang Hu" <hu@...>
Cc: Gbrowse Mailing List <gmod-gbrowse@...>
Message-ID:
	<bdd134570811031127s3dd0e908s50730e7619ac9e80@...>
Content-Type: text/plain; charset=ISO-8859-1

Hi,

Are your "html1 = ", etc., args in the [GENERAL] section?   Any new
stanza's (that start with a '[stanza name]' in square brackets)
introduced too early will disable any top-level config in the
[GENERAL]  section.

Sheldon

On Mon, Nov 3, 2008 at 2:08 PM, Zhiliang Hu <hu@...> wrote:
> In a process to get popup balloon out, I found basic html tags fail to
> show up:
>
> balloon tips = 1
>
> ### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ###
> # inside the <head></head> section
> head = <title>Cattle Genome Track</title>
> # at the top...
> header = <h1>Cattle Genome Track - Chromosome 8 </h1>
> footer = <h1>add footer</h1>
> #footer = sub {
> #               my $file =
"/usr/local/apache/doc/default/trailerb.tmpl";
> #               my $tailout;
> #               if (-e $file) {
> #                 open(FILE, "$file");
> #                   while (<FILE>) {
> #                     $tailout .= "$_";
> #                   }
> #                 close(FILE);
> #               } else {
> #                   $tailout = "<font color=red>Trailerb not
found</font>";
> #               }
> #               return ($tailout);
> #             }
> # Various places where you can insert your own HTML -- see
configuration docs
> html1 = <h2> html1</h2>
> html2 = <h2> Html2</h2>
> html3 = <h2> Html3</h2>
> html4 = <h2> Html4</h2>
> html5 = <h2> Html5</h2>
> html6 = <h2> Html6</h2>
>
> I tried to back up by reducing my conf file to see what's going on but
do
> not find clues/lucks.  They stay not shown.  What could be the cause?
> (Not the browser/cache problem).
>
> Thanks,
> Zhiliang
>
>
------------------------------------------------------------------------
-
> This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
> Build the coolest Linux based applications with Moblin SDK & win great
prizes
> Grand prize is a trip for two to an Open Source event anywhere in the
world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

-- 
Sheldon J. McKay, PhD
Research Investigator
Cold Spring Harbor Laboratory
Office: 516-367-6998
Fax: 516 367-6851
Email: mckays@...
Skype: mckays630

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

------------------------------------------------------------------------
-
This SF.Net email is sponsored by the Moblin Your Move Developer's
challenge
Build the coolest Linux based applications with Moblin SDK & win great
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world
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Zhiliang Hu | 3 Nov 21:30 2008

Re: simple but weird problem

Thanks Sheldon,

Yes. all my cited contents are in [GENERAL] section; and all these tags 
are not repeated in the rest of the conf file (or any other "stanza"). -- 
Does that clear this possibility?  Or you meant something else?

Zhiliang

On Mon, 3 Nov 2008, Sheldon McKay wrote:

> Date: Mon, 3 Nov 2008 14:27:59 -0500
> From: Sheldon McKay <sheldon.mckay@...>
> Reply-To: mckays@...
> To: Zhiliang Hu <hu@...>
> Cc: Gbrowse Mailing List <gmod-gbrowse@...>
> Subject: Re: [Gmod-gbrowse] simple but weird problem
> 
> Hi,
>
> Are your "html1 = ", etc., args in the [GENERAL] section?   Any new
> stanza's (that start with a '[stanza name]' in square brackets)
> introduced too early will disable any top-level config in the
> [GENERAL]  section.
>
> Sheldon
>
> On Mon, Nov 3, 2008 at 2:08 PM, Zhiliang Hu <hu@...> wrote:
>> In a process to get popup balloon out, I found basic html tags fail to
>> show up:
>>
>> balloon tips = 1
>>
>> ### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ###
>> # inside the <head></head> section
>> head = <title>Cattle Genome Track</title>
>> # at the top...
>> header = <h1>Cattle Genome Track - Chromosome 8 </h1>
>> footer = <h1>add footer</h1>
>> #footer = sub {
>> #               my $file = "/usr/local/apache/doc/default/trailerb.tmpl";
>> #               my $tailout;
>> #               if (-e $file) {
>> #                 open(FILE, "$file");
>> #                   while (<FILE>) {
>> #                     $tailout .= "$_";
>> #                   }
>> #                 close(FILE);
>> #               } else {
>> #                   $tailout = "<font color=red>Trailerb not found</font>";
>> #               }
>> #               return ($tailout);
>> #             }
>> # Various places where you can insert your own HTML -- see configuration docs
>> html1 = <h2> html1</h2>
>> html2 = <h2> Html2</h2>
>> html3 = <h2> Html3</h2>
>> html4 = <h2> Html4</h2>
>> html5 = <h2> Html5</h2>
>> html6 = <h2> Html6</h2>
>>
>> I tried to back up by reducing my conf file to see what's going on but do
>> not find clues/lucks.  They stay not shown.  What could be the cause?
>> (Not the browser/cache problem).
>>
>> Thanks,
>> Zhiliang
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
>

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Scott Cain | 3 Nov 21:33 2008
Picon

Re: converting Promer (Mummer) output files to GFF

Hi Shalabh,

I don't know of any; try asking on the bioperl mailing list.  There
are several parsers that are part of BioPerl, and there might be one
that would work with Promer.

http://www.bioperl.org/wiki/Mailing_lists

Scott

On Mon, Nov 3, 2008 at 3:15 PM, shalabh sharma
<shalabh.sharma7@...> wrote:
> Hi All,
>             Is there any way we can convert output files from Promer
> (Mummer) to GFF format?
>
> Thanks
> Shalabh
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

--

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

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Gmane