[Bioperl-l] [Gmod-gbrowse] bioperl-live & annotator plugin
Lincoln Stein
lincoln.stein at gmail.com
Tue Dec 2 15:51:06 UTC 2008
I take it back. You should add the matrix in add_type(), assuming that
$matrix is some sort of descriptive term.
Lincoln
On Tue, Dec 2, 2008 at 10:49 AM, Lincoln Stein <lincoln.stein at gmail.com>wrote:
> 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
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724 USA
> (516) 367-8380
> Assistant: Sandra Michelsen <michelse at cshl.edu>
>
--
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
1 Bungtown Road
Cold Spring Harbor, NY 11724 USA
(516) 367-8380
Assistant: Sandra Michelsen <michelse at cshl.edu>
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