Re: balloon tips

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Re: balloon tips

Sheldon McKay
Could you please provide an example of your config file showing exactly what
you are trying to do?

It sounds like you are trying to interpolate variables that exist only
within the callback shown in your config file snippet, so $extra, for
example, will only exist if you call the pre-defined 'intro' function as your
balloon hover option, not outside of it.

A simple way to access the Note in a callback would be would be:

balloon hover = sub {
  my $feat = shift;
  my $note = join(' ',$feat->each_tag_value('Note')) if $feat->has_tag('Note');
  return $note  }


Sheldon McKay, PhD
Scientific Lead, iPlant Collaborative
BIO5 Institute, University of Arizona
Email: [hidden email]
Google Voice:  (203) 701-9204



On Mon, Mar 28, 2011 at 8:43 AM,  <[hidden email]> wrote:

> Hello Sheldon,
>
> Did you get the balloon hover show 'Note' feature. I am trying to do the same but it won't work.
>
> Thank for any help.
> Cheers,
> Purnima
>
> <quote author='Sheldon McKay'>
> Hi Sean,
>
> A few variables get interpolated when encountered as bare text in a
> config options but, generally, non-word characters, such as '$' will
> be removed or escaped.  For your second and third examples, I think
> you need to wrap them in perl callbacks, with the variables explicitly
> populated.
>
> Sheldon
>
> On Mon, Nov 17, 2008 at 12:39 PM, Sean O'Keeffe <[hidden email]>
> wrote:
>> Hi all,
>> I'm having a little issue with Balloon tips in Hover mode.
>> I can only ever get $name, $start & $end displayed in the balloon.
>> I've tried everything to get $score and/or $extra( i.e. 'Alias' or
>> 'Note') to work but to no avail.
>>
>> In the [TRACK DEFULTS] section:
>> balloon hover = <b>$start - $end</b> ($name)     # works a treat
>> balloon hover = <b>$extra</b> ($score)             # prints out the
>> words extra and (score)
>> balloon hover = <b>$feat->each_tag_value('Alias')</b>($feat->score) #
>> again prints feat->each_tag_value('Alias') (score)
>>
>> [TOOLTIPS]      # never touched these - come as standard
>> intro = sub {
>>                my $args  = shift;
>>                my $feat  = $args->{feature};
>>                my $name  = $feat->display_name;
>>                my $type  = $feat->primary_tag;
>>                my $class = $feat->class;
>>                my $score = $feat->score;
>>                my $extra = join(' ',$feat->each_tag_value('Note')) if
>> $feat->has_tag('Note');
>>                my $n     = $type =~ /^[AEIOU]/i ? 'n' : '';
>>                my $msg   = "Hello, I am $name, a$n $type of class $class";
>>                $msg     .= "<br>I am described as a <b>$extra</b><br>"
>> if $extra;
>>                my $seq   = substr $feat->seq->seq, 0, 400;
>>                $seq =~ s/(\S{50})/$1\n/g;
>>                return "<table><tr><th
>> bgcolor='lightsteelblue'>$name</th><tr>" .
>>                       "<tr><td>$msg</td></tr><tr><td
>> bgcolor='lightyellow'>".
>>                       "First 400 bp (click on $type $name for the full
>> sequence):".
>>               "<br><pre>>$name\n$seq</pre></td></tr></table>";
>>           }
>>
>>
>> Has anyone had such issues?
>>
>> Thanks,
>> Sean.
>>
>> -------------------------------------------------------------------------
>> 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
>> [hidden email]
>> 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: [hidden email]
> 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
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
> </quote>
> Quoted from:
> http://generic-model-organism-system-database.450254.n5.nabble.com/balloon-tips-tp454793p454794.html
>

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Re: balloon tips

pachorip
Hello Sheldon,

Thank you for your quick reply,

Following is a part of my gff file:

I am using processed_transcript as aggregator. I basically want to see
as label, the fpkm values (which are present in 9th column of mRNA
features):

##gff-version 3
27371   Castor_lane1    CDS     1035    1649    .       +       1
Parent=27371.m000068  
27371   Castor_lane1    CDS     142     404     .       +       0
Parent=27371.m000068  
27371   Castor_lane1    CDS     1682    1809    .       +       1
Parent=27371.m000068  
27371   Castor_lane1    CDS     6556    7503    .       -       0
Parent=27371.m000069  
27371   Castor_lane1    CDS     7613    7894    .       +       0
Parent=27371.m000070  
27371   Castor_lane1    CDS     8018    8324    .       +       0
Parent=27371.m000071  
27371   Castor_lane1    CDS     821     960     .       +       2
Parent=27371.m000068  
27371   Castor_lane1    CDS     8390    8754    .       +       1
Parent=27371.m000071  
27371   Castor_lane1    exon    1035    1649    .       +       .
Parent=27371.m000068  
27371   Castor_lane1    exon    142     404     .       +       .
Parent=27371.m000068  
27371   Castor_lane1    exon    1682    1809    .       +       .
Parent=27371.m000068  
27371   Castor_lane1    exon    6556    7503    .       -       .
Parent=27371.m000069  
27371   Castor_lane1    exon    7613    7894    .       +       .
Parent=27371.m000070  
27371   Castor_lane1    exon    8018    8324    .       +       .
Parent=27371.m000071  
27371   Castor_lane1    exon    821     960     .       +       .
Parent=27371.m000068  
27371   Castor_lane1    exon    8390    8754    .       +       .
Parent=27371.m000071  
27371   Castor_lane1    gene    142     1809    .       +       .
ID=27371.t000001;Name=27371.t000001;Note=conserved hypothetical protein;
27371   Castor_lane1    gene    6556    7503    .       -       .
ID=27371.t000002;Name=27371.t000002;Note=conserved hypothetical protein;
27371   Castor_lane1    gene    7613    7894    .       +       .
ID=27371.t000003;Name=27371.t000003;Note=conserved hypothetical protein;
27371   Castor_lane1    gene    8018    8754    .       +       .
ID=27371.t000004;Name=27371.t000004;Note=conserved hypothetical protein;
27371   Castor_lane1    mRNA    142     1809    .       +       .
ID=27371.m000068;Name=27371.m000068;Parent=27371.t000001;Note=conserved
hypothetical protein;fpkm=0;
27371   Castor_lane1    mRNA    6556    7503    .       -       .
ID=27371.m000069;Name=27371.m000069;Parent=27371.t000002;Note=conserved
hypothetical protein;fpkm=6.778;
27371   Castor_lane1    mRNA    7613    7894    .       +       .
ID=27371.m000070;Name=27371.m000070;Parent=27371.t000003;Note=conserved
hypothetical protein;fpkm=2.225;
27371   Castor_lane1    mRNA    8018    8754    .       +       .
ID=27371.m000071;Name=27371.m000071;Parent=27371.t000004;Note=conserved
hypothetical protein;fpkm=0;
27371   Castor_lane1    start_codon     142     144     .
+       .       Parent=27371.m000068  
27371   Castor_lane1    start_codon     6556    6558    .
-       .       Parent=27371.m000069  
27371   Castor_lane1    start_codon     7613    7615    .
+       .       Parent=27371.m000070  
27371   Castor_lane1    start_codon     8018    8020    .
+       .       Parent=27371.m000071  
27371   Castor_lane1    stop_codon      1807    1809    .
+       .       Parent=27371.m000068  
27371   Castor_lane1    stop_codon      7501    7503    .
-       .       Parent=27371.m000069  
27371   Castor_lane1    stop_codon      7892    7894    .
+       .       Parent=27371.m000070  
27371   Castor_lane1    stop_codon      8752    8754    .
+       .       Parent=27371.m000071  

Following is the part of config file :

[mRNA_lane1]
feature        = processed_transcript:Castor_lane1
database    = annotations
glyph          = processed_transcript
bgcolor   = blue
fgcolor = blue
utr_color = lightblue
thin_utr = 0
height         = 9
description     = 1
label = 1
label density =50
bump density =150
category       = Castor Lanes:mRNAs
key            = mRNA from Developing endosperm_5_6

I have tried the balloon hover code, but it just shows part of Note just
before fpkm.

It would be great if I can show these fpkm values in the label, if not
in the balloon hover.

Cheers,
P.
On Mon, 2011-03-28 at 16:18 +0100, Sheldon McKay wrote:

> Could you please provide an example of your config file showing exactly what
> you are trying to do?
>
> It sounds like you are trying to interpolate variables that exist only
> within the callback shown in your config file snippet, so $extra, for
> example, will only exist if you call the pre-defined 'intro' function as your
> balloon hover option, not outside of it.
>
> A simple way to access the Note in a callback would be would be:
>
> balloon hover = sub {
>   my $feat = shift;
>   my $note = join(' ',$feat->each_tag_value('Note')) if $feat->has_tag('Note');
>   return $note  }
>
>
> Sheldon McKay, PhD
> Scientific Lead, iPlant Collaborative
> BIO5 Institute, University of Arizona
> Email: [hidden email]
> Google Voice:  (203) 701-9204
>
>
>
> On Mon, Mar 28, 2011 at 8:43 AM,  <[hidden email]> wrote:
> > Hello Sheldon,
> >
> > Did you get the balloon hover show 'Note' feature. I am trying to do the same but it won't work.
> >
> > Thank for any help.
> > Cheers,
> > Purnima
> >
> > <quote author='Sheldon McKay'>
> > Hi Sean,
> >
> > A few variables get interpolated when encountered as bare text in a
> > config options but, generally, non-word characters, such as '$' will
> > be removed or escaped.  For your second and third examples, I think
> > you need to wrap them in perl callbacks, with the variables explicitly
> > populated.
> >
> > Sheldon
> >
> > On Mon, Nov 17, 2008 at 12:39 PM, Sean O'Keeffe <[hidden email]>
> > wrote:
> >> Hi all,
> >> I'm having a little issue with Balloon tips in Hover mode.
> >> I can only ever get $name, $start & $end displayed in the balloon.
> >> I've tried everything to get $score and/or $extra( i.e. 'Alias' or
> >> 'Note') to work but to no avail.
> >>
> >> In the [TRACK DEFULTS] section:
> >> balloon hover = <b>$start - $end</b> ($name)     # works a treat
> >> balloon hover = <b>$extra</b> ($score)             # prints out the
> >> words extra and (score)
> >> balloon hover = <b>$feat->each_tag_value('Alias')</b>($feat->score) #
> >> again prints feat->each_tag_value('Alias') (score)
> >>
> >> [TOOLTIPS]      # never touched these - come as standard
> >> intro = sub {
> >>                my $args  = shift;
> >>                my $feat  = $args->{feature};
> >>                my $name  = $feat->display_name;
> >>                my $type  = $feat->primary_tag;
> >>                my $class = $feat->class;
> >>                my $score = $feat->score;
> >>                my $extra = join(' ',$feat->each_tag_value('Note')) if
> >> $feat->has_tag('Note');
> >>                my $n     = $type =~ /^[AEIOU]/i ? 'n' : '';
> >>                my $msg   = "Hello, I am $name, a$n $type of class $class";
> >>                $msg     .= "<br>I am described as a <b>$extra</b><br>"
> >> if $extra;
> >>                my $seq   = substr $feat->seq->seq, 0, 400;
> >>                $seq =~ s/(\S{50})/$1\n/g;
> >>                return "<table><tr><th
> >> bgcolor='lightsteelblue'>$name</th><tr>" .
> >>                       "<tr><td>$msg</td></tr><tr><td
> >> bgcolor='lightyellow'>".
> >>                       "First 400 bp (click on $type $name for the full
> >> sequence):".
> >>               "<br><pre>>$name\n$seq</pre></td></tr></table>";
> >>           }
> >>
> >>
> >> Has anyone had such issues?
> >>
> >> Thanks,
> >> Sean.
> >>
> >> -------------------------------------------------------------------------
> >> 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
> >> [hidden email]
> >> 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: [hidden email]
> > 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
> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
> > </quote>
> > Quoted from:
> > http://generic-model-organism-system-database.450254.n5.nabble.com/balloon-tips-tp454793p454794.html
> >



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Re: balloon tips

Sheldon McKay
You are using  fpkm as a tag.  you can modify the callback to use that
tag instead of Note, or to use both tags.
or replace the semicolon before  fpkm with a comma.

Sheldon

Sheldon McKay, PhD
Scientific Lead, iPlant Collaborative
BIO5 Institute, University of Arizona
Email: [hidden email]
Google Voice:  (203) 701-9204



On Mon, Mar 28, 2011 at 11:37 AM, PURNIMA PACHORI
<[hidden email]> wrote:

> Hello Sheldon,
>
> Thank you for your quick reply,
>
> Following is a part of my gff file:
>
> I am using processed_transcript as aggregator. I basically want to see
> as label, the fpkm values (which are present in 9th column of mRNA
> features):
>
> ##gff-version 3
> 27371   Castor_lane1    CDS     1035    1649    .       +       1
> Parent=27371.m000068
> 27371   Castor_lane1    CDS     142     404     .       +       0
> Parent=27371.m000068
> 27371   Castor_lane1    CDS     1682    1809    .       +       1
> Parent=27371.m000068
> 27371   Castor_lane1    CDS     6556    7503    .       -       0
> Parent=27371.m000069
> 27371   Castor_lane1    CDS     7613    7894    .       +       0
> Parent=27371.m000070
> 27371   Castor_lane1    CDS     8018    8324    .       +       0
> Parent=27371.m000071
> 27371   Castor_lane1    CDS     821     960     .       +       2
> Parent=27371.m000068
> 27371   Castor_lane1    CDS     8390    8754    .       +       1
> Parent=27371.m000071
> 27371   Castor_lane1    exon    1035    1649    .       +       .
> Parent=27371.m000068
> 27371   Castor_lane1    exon    142     404     .       +       .
> Parent=27371.m000068
> 27371   Castor_lane1    exon    1682    1809    .       +       .
> Parent=27371.m000068
> 27371   Castor_lane1    exon    6556    7503    .       -       .
> Parent=27371.m000069
> 27371   Castor_lane1    exon    7613    7894    .       +       .
> Parent=27371.m000070
> 27371   Castor_lane1    exon    8018    8324    .       +       .
> Parent=27371.m000071
> 27371   Castor_lane1    exon    821     960     .       +       .
> Parent=27371.m000068
> 27371   Castor_lane1    exon    8390    8754    .       +       .
> Parent=27371.m000071
> 27371   Castor_lane1    gene    142     1809    .       +       .
> ID=27371.t000001;Name=27371.t000001;Note=conserved hypothetical protein;
> 27371   Castor_lane1    gene    6556    7503    .       -       .
> ID=27371.t000002;Name=27371.t000002;Note=conserved hypothetical protein;
> 27371   Castor_lane1    gene    7613    7894    .       +       .
> ID=27371.t000003;Name=27371.t000003;Note=conserved hypothetical protein;
> 27371   Castor_lane1    gene    8018    8754    .       +       .
> ID=27371.t000004;Name=27371.t000004;Note=conserved hypothetical protein;
> 27371   Castor_lane1    mRNA    142     1809    .       +       .
> ID=27371.m000068;Name=27371.m000068;Parent=27371.t000001;Note=conserved
> hypothetical protein;fpkm=0;
> 27371   Castor_lane1    mRNA    6556    7503    .       -       .
> ID=27371.m000069;Name=27371.m000069;Parent=27371.t000002;Note=conserved
> hypothetical protein;fpkm=6.778;
> 27371   Castor_lane1    mRNA    7613    7894    .       +       .
> ID=27371.m000070;Name=27371.m000070;Parent=27371.t000003;Note=conserved
> hypothetical protein;fpkm=2.225;
> 27371   Castor_lane1    mRNA    8018    8754    .       +       .
> ID=27371.m000071;Name=27371.m000071;Parent=27371.t000004;Note=conserved
> hypothetical protein;fpkm=0;
> 27371   Castor_lane1    start_codon     142     144     .
> +       .       Parent=27371.m000068
> 27371   Castor_lane1    start_codon     6556    6558    .
> -       .       Parent=27371.m000069
> 27371   Castor_lane1    start_codon     7613    7615    .
> +       .       Parent=27371.m000070
> 27371   Castor_lane1    start_codon     8018    8020    .
> +       .       Parent=27371.m000071
> 27371   Castor_lane1    stop_codon      1807    1809    .
> +       .       Parent=27371.m000068
> 27371   Castor_lane1    stop_codon      7501    7503    .
> -       .       Parent=27371.m000069
> 27371   Castor_lane1    stop_codon      7892    7894    .
> +       .       Parent=27371.m000070
> 27371   Castor_lane1    stop_codon      8752    8754    .
> +       .       Parent=27371.m000071
>
> Following is the part of config file :
>
> [mRNA_lane1]
> feature        = processed_transcript:Castor_lane1
> database    = annotations
> glyph          = processed_transcript
> bgcolor   = blue
> fgcolor = blue
> utr_color = lightblue
> thin_utr = 0
> height         = 9
> description     = 1
> label = 1
> label density =50
> bump density =150
> category       = Castor Lanes:mRNAs
> key            = mRNA from Developing endosperm_5_6
>
> I have tried the balloon hover code, but it just shows part of Note just
> before fpkm.
>
> It would be great if I can show these fpkm values in the label, if not
> in the balloon hover.
>
> Cheers,
> P.
> On Mon, 2011-03-28 at 16:18 +0100, Sheldon McKay wrote:
>> Could you please provide an example of your config file showing exactly what
>> you are trying to do?
>>
>> It sounds like you are trying to interpolate variables that exist only
>> within the callback shown in your config file snippet, so $extra, for
>> example, will only exist if you call the pre-defined 'intro' function as your
>> balloon hover option, not outside of it.
>>
>> A simple way to access the Note in a callback would be would be:
>>
>> balloon hover = sub {
>>   my $feat = shift;
>>   my $note = join(' ',$feat->each_tag_value('Note')) if $feat->has_tag('Note');
>>   return $note  }
>>
>>
>> Sheldon McKay, PhD
>> Scientific Lead, iPlant Collaborative
>> BIO5 Institute, University of Arizona
>> Email: [hidden email]
>> Google Voice:  (203) 701-9204
>>
>>
>>
>> On Mon, Mar 28, 2011 at 8:43 AM,  <[hidden email]> wrote:
>> > Hello Sheldon,
>> >
>> > Did you get the balloon hover show 'Note' feature. I am trying to do the same but it won't work.
>> >
>> > Thank for any help.
>> > Cheers,
>> > Purnima
>> >
>> > <quote author='Sheldon McKay'>
>> > Hi Sean,
>> >
>> > A few variables get interpolated when encountered as bare text in a
>> > config options but, generally, non-word characters, such as '$' will
>> > be removed or escaped.  For your second and third examples, I think
>> > you need to wrap them in perl callbacks, with the variables explicitly
>> > populated.
>> >
>> > Sheldon
>> >
>> > On Mon, Nov 17, 2008 at 12:39 PM, Sean O'Keeffe <[hidden email]>
>> > wrote:
>> >> Hi all,
>> >> I'm having a little issue with Balloon tips in Hover mode.
>> >> I can only ever get $name, $start & $end displayed in the balloon.
>> >> I've tried everything to get $score and/or $extra( i.e. 'Alias' or
>> >> 'Note') to work but to no avail.
>> >>
>> >> In the [TRACK DEFULTS] section:
>> >> balloon hover = <b>$start - $end</b> ($name)     # works a treat
>> >> balloon hover = <b>$extra</b> ($score)             # prints out the
>> >> words extra and (score)
>> >> balloon hover = <b>$feat->each_tag_value('Alias')</b>($feat->score) #
>> >> again prints feat->each_tag_value('Alias') (score)
>> >>
>> >> [TOOLTIPS]      # never touched these - come as standard
>> >> intro = sub {
>> >>                my $args  = shift;
>> >>                my $feat  = $args->{feature};
>> >>                my $name  = $feat->display_name;
>> >>                my $type  = $feat->primary_tag;
>> >>                my $class = $feat->class;
>> >>                my $score = $feat->score;
>> >>                my $extra = join(' ',$feat->each_tag_value('Note')) if
>> >> $feat->has_tag('Note');
>> >>                my $n     = $type =~ /^[AEIOU]/i ? 'n' : '';
>> >>                my $msg   = "Hello, I am $name, a$n $type of class $class";
>> >>                $msg     .= "<br>I am described as a <b>$extra</b><br>"
>> >> if $extra;
>> >>                my $seq   = substr $feat->seq->seq, 0, 400;
>> >>                $seq =~ s/(\S{50})/$1\n/g;
>> >>                return "<table><tr><th
>> >> bgcolor='lightsteelblue'>$name</th><tr>" .
>> >>                       "<tr><td>$msg</td></tr><tr><td
>> >> bgcolor='lightyellow'>".
>> >>                       "First 400 bp (click on $type $name for the full
>> >> sequence):".
>> >>               "<br><pre>>$name\n$seq</pre></td></tr></table>";
>> >>           }
>> >>
>> >>
>> >> Has anyone had such issues?
>> >>
>> >> Thanks,
>> >> Sean.
>> >>
>> >> -------------------------------------------------------------------------
>> >> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> >> challenge
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>> >> world
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>> >> _______________________________________________
>> >> Gmod-gbrowse mailing list
>> >> [hidden email]
>> >> 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: [hidden email]
>> > 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
>> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> > _______________________________________________
>> > Gmod-gbrowse mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> >
>> > </quote>
>> > Quoted from:
>> > http://generic-model-organism-system-database.450254.n5.nabble.com/balloon-tips-tp454793p454794.html
>> >
>
>
>

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