question about give different color glyph to entries that are in the same feature

[陈冠华]

Hi all,

If I want that for different ID pattern, the graph display different color,what should I do, since I try my code as follows but it does not work:

feature      = region:omim
glyph        = box
bgcolor      = sub {    my $f = shift; my ($name) = $f->attributes('ID');
                               if ($name =~ /omim/) {return 'cyan' ;}
                               retun 'red';
}

The data is like following:

chr1    omim    region    1224571    144979554    .    +    .    ID=decipher4083;Note=1q21.1 recurrent microduplication (possible susceptiblity locus for neurodevelopmental disorders)
chr1    omim    region    2149993    2231511    .    +    .    ID=omim1949;omimgene=164780;omimdisease=0;gene=SKI;Note=SKI-1p36 deletion syndrome

The error_log shows the following error:
An error occurred while evaluating the callback at section='OMIM', option='bgcolor':, referer: http://trish.med.unc.edu/cgi-bin/gb2/gbrowse/SLEP/
 => Missing right curly or square bracket at (eval 91) line 4, at end of line, referer: http://trish.med.unc.edu/cgi-bin/gb2/gbrowse/SLEP/
 syntax error at (eval 91) line 4, at EOF, referer: http://trish.med.unc.edu/cgi-bin/gb2/gbrowse/SLEP/
 at /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm line 245, referer: http://trish.med.unc.edu/cgi-bin/gb2/gbrowse/SLEP/

Thank you very much!

Yours
Josh

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[Dave Clements, GMOD Help Desk]

Hi Josh,

I think the problem is that the } on the last line does not have any
whitespace in front of it.  Add a blank or a tab and rerun.  GBrowse
treats anything that starts with leading whitespace as a continuation
of the previous line.

Dave C.

On Wed, Sep 9, 2009 at 8:11 PM, 陈冠华 <cghhust@...> wrote:

> Hi all,
>
> If I want that for different ID pattern, the graph display different
> color,what should I do, since I try my code as follows but it does not work:
>
> feature      = region:omim
> glyph        = box
> bgcolor      = sub {    my $f = shift; my ($name) = $f->attributes('ID');
>                                if ($name =~ /omim/) {return 'cyan' ;}
>                                retun 'red';
> }
>
> The data is like following:
>
> chr1    omim    region    1224571    144979554    .    +    .
> ID=decipher4083;Note=1q21.1 recurrent microduplication (possible
> susceptiblity locus for neurodevelopmental disorders)
> chr1    omim    region    2149993    2231511    .    +    .
> ID=omim1949;omimgene=164780;omimdisease=0;gene=SKI;Note=SKI-1p36 deletion
> syndrome
>
> The error_log shows the following error:
> An error occurred while evaluating the callback at section='OMIM',
> option='bgcolor':, referer:
> http://trish.med.unc.edu/cgi-bin/gb2/gbrowse/SLEP/
>  => Missing right curly or square bracket at (eval 91) line 4, at end of
> line, referer: http://trish.med.unc.edu/cgi-bin/gb2/gbrowse/SLEP/
>  syntax error at (eval 91) line 4, at EOF, referer:
> http://trish.med.unc.edu/cgi-bin/gb2/gbrowse/SLEP/
>  at
> /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> line 245, referer: http://trish.med.unc.edu/cgi-bin/gb2/gbrowse/SLEP/
>
> Thank you very much!
>
> Yours
> Josh
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

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