[Bioperl-l] Bio::Graphics heterogeneous_segments problem.
Marco Aurelio Valtas Cunha
mavcunha at gordon.fmrp.usp.br
Thu Feb 13 08:48:24 EST 2003
Lincoln,
Thank you, I will update bioperl-live right now.
Marco.
Lincoln Stein wrote:
> Hi Marco,
>
> The latest bunch of commits I made to the bioperl 1.2 live branch fixes the
> problem you found.
>
> Lincoln
>
>
> On Monday 03 February 2003 02:25 pm, Marco Aurelio Valtas Cunha wrote:
>
>>Hi all,
>>
>> If you work with bigger SeqFeatures the end graph is not rendered. If
>>run this script (bellow) you'll get something like:
>>
>>----XXXXXXXXXX------
>>
>>But when you mutiply the constants by ten, the graph render like:
>>
>>----XXXXXXXXXX
>>
>>no end tail.
>>PS: All GD, libgd and Bio::Graphics are up to date.
>>
>>Thanks Marco.
>>
>>
>>use strict;
>>use warnings;
>>use Bio::Graphics;
>>use Bio::SeqFeature::Generic;
>>
>># Some test coord.
>>use constant I_SIZE => 200;
>>use constant E_START => 50;
>>use constant E_END => 150;
>>
>>my $intron = Bio::SeqFeature::Generic->new(
>> -primary => 'region_2',
>> -start => '0',
>> -end => I_SIZE,
>> -strand => 1,
>> -source => 'intron',
>>);
>>
>>my $exon = Bio::SeqFeature::Generic->new(
>> -primary => '',
>> -start => E_START,
>> -end => E_END,
>> -source => 'exon',
>>);
>>$intron->add_sub_SeqFeature($exon);
>>
>>my $graphics = Bio::Graphics::Panel->new(
>> -segment => $intron,
>> -width => '200',
>>);
>>
>>$graphics->add_track(
>> heterogeneous_segments => $intron,
>> -fgcolor => 'black',
>> -exon_color => 'red',
>> -height => 8,
>>);
>>
>>print $graphics->png;
>
>
--
Marco A Valtas Cunha http://scarecrow.fmrp.usp.br/~mavcunha/
Lab de Bioinformatica http://bit.fmrp.usp.br
Hemocentro de Rib Preto http://ctc.fmrp.usp.br
Fax: 55 16 3963-9309 Tel: 55 16 3963-9300 R:9603
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