[Bioperl-l] [Gmod-gbrowse] bioperl-live & annotator plugin

Lincoln Stein lincoln.stein at gmail.com
Tue Dec 2 15:49:45 UTC 2008


Hi Sean,

Did your plugin break when you upgraded to GBrowse 1.7, or when you upgraded
bioperl? Knowing this will help me figure out where to look for the problem.
It frankly looks like a database problem in the sense that the xyplot glyph
is trying to render 100 features rather than a feature with 100 parts.

Are you sure this step is correct?

$feature_list->add_type($matrix=>{glyph   => 'xyplot',
>                       graph_type => 'boxes',
>                   scale   => 'auto',
>                   height => 40,
>                   bump => 0,
>                   min_score=>0,
>                   max_score=>$maxscore,
>                   key     => "$matrix affinities ($maxscore)",
>                   fgcolor => $COLORS[$i % @COLORS],
>                   bgcolor => $COLORS[$i % @COLORS],
>                   });


It seems to me you intend to add the $feature, not the $matrix variable.

Lincoln

On Tue, Dec 2, 2008 at 10:32 AM, Sean O'Keeffe <okeeffe at molgen.mpg.de>wrote:

> Hi all,
> I'm experiencing a little issue when upgrading to the latest bioperl-live
> build.
> We needed the new glyph libraries as older versions can't display wiggle
> density plots and also experience versioning issues for Gbrowse 1.7.
> On upgrading to the latest nightly build, all seemed fine until we tried
> our TF affinity annotator plugin.
> The plugin basically generates GFF output of a selected matrix binding to
> the sequence of the current window, and displays the score values as an
> xyplot.
> We've never had any real issues 'til the new libraries were loaded. I tried
> switching the old xyplot.pm with the new one but to no avail.
> I've attached 2 images old and new of the generated output, plus some code
> and feature file output.
> Any insight would be great,
>
> Sean.
>
> +++++++++++++++++++++++++++++++++++++++++++++++++++
>
> the code of interest in the plugin
>
> ......
>  my $i = 0;
>  my (@features,$feature,$start,$end,$score,$maxscore,$strand);
>  $feature_list = Bio::Graphics::FeatureFile->new();
>
>  foreach $matrix (@matrices){
>   $maxscore=0;
>   # Usually the track is created first but here we want the maxscore passed
> to
>   # the track so we process the features first and create the track after.
>   foreach $_ (@result){
>     next if (/\#/);
>     next unless (/$matrix/);
>     @features = split("\t", $_);
>
> $start=$features[3];$end=$features[4];$score=$features[5];$strand=$features[6];
>     if ($score>$maxscore) {
>       $maxscore=$score;
>     }
>     # Fill the feature list with features
>     $feature = Bio::Graphics::Feature->new(-start=>$abs_start + $start,
>                             -stop=>$abs_start + $end,
>                       -score=>$score,
>                       -strand=>$strand,
>                       -ref=>$ref,
>                       -name=>$matrix,
>                       -type=>'region',
>                       -source=>'ANNOTATE');
>     $feature_list->add_feature($feature,$matrix);
>   }
>     # Create the track and add features
>   $feature_list->add_type($matrix=>{glyph   => 'xyplot',
>                       graph_type => 'boxes',
>                   scale   => 'auto',
>                   height => 40,
>                   bump => 0,
>                   min_score=>0,
>                   max_score=>$maxscore,
>                   key     => "$matrix affinities ($maxscore)",
>                   fgcolor => $COLORS[$i % @COLORS],
>                   bgcolor => $COLORS[$i % @COLORS],
>                   });
>   $i++;
>  }
>  return $feature_list;
> .........
>
> +++++++++++++++++++++++++++++++++++++++++++
>
> the feature file which is passed to the plugin
>
> #command_line= /project/gbrowse/Pipeline/Annotation/ANNOTATE_v2.07 -s
> /project/general/tmp/TIwySJV5kx --pscm /project/general/tmp/FkztCDpBvb -name
> SRF_C -a -g 0.5 -t 0 -R 200 -S 100 -p 1.0
> segment ANNOTATE        region  1       200     0.000103017     +       .
>     matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200
> segment ANNOTATE        region  101     300     0.000101877     +       .
>     matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200
> segment ANNOTATE        region  201     400     6.76318e-05     +       .
>     matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200
> segment ANNOTATE        region  301     500     7.0194e-05      +       .
>     matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200
> segment ANNOTATE        region  401     600     3.36309e-05     +       .
>     matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200
> segment ANNOTATE        region  501     700     7.15977e-05     +       .
>     matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200
> segment ANNOTATE        region  601     800     0.000639066     +       .
>     matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200
> segment ANNOTATE        region  701     900     0.000589631     +       .
>     matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200
> segment ANNOTATE        region  801     1000    0.000580096     +       .
>     matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200
> segment ANNOTATE        region  901     1100    0.00139282      +       .
>     matrix_id=M00215;matrix_name='V$SRF_C';seq_id=segment;def_L=200
> ...
>
>
>
>
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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 at oicr.on.ca>

Cold Spring Harbor Laboratory
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(516) 367-8380
Assistant: Sandra Michelsen <michelse at cshl.edu>



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