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
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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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>>>
>>
>>
>> --
>>
------------------------------------------------------------------------
>> 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
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>> Build the coolest Linux based applications with Moblin SDK & win
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>>
>
>
>
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> Build the coolest Linux based applications with Moblin SDK & win great
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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@...>
-------------- next part --------------
An HTML attachment was scrubbed...
------------------------------
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
prizes
Grand prize is a trip for two to an Open Source event anywhere in the
world
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