Re: error messages due to added code in the init_code

No. They are pretty simple implementations. Please find below one of them (BCS_GGB_Util.pm)

package BCS_GGB_Util;
use strict;
use warnings;
use diagnostics;

use vars qw(@ISA @EXPORT);

require Exporter;
@ISA = 'Exporter';
@EXPORT = qw(
    gene_bgcolor
    gene_fgcolor
    codon_bgcolor
        );

use constant DEBUG => 0;

sub codon_bgcolor{
    my $feature = shift;
    my @name    = $feature->attributes('Charge');
    if (grep(/(acidic)/i, @name)) {
        return 'red';
    }
    elsif (grep(/(basic)/i, @name)) {
        return 'blue';
    }
    elsif (grep(/(nonpolar_neutral)/i, @name)) {
        return 'green';
    }
     elsif (grep(/(polar_neutral)/i, @name)) {
        return 'yellow';
    }
    else {
        return 'black';
    }
}

sub gene_bgcolor{
    my $feature = shift;
    my @name    = $feature->attributes('SubjectDescription');
    if (grep(/(transpos)|(repeat)|(repeti)/i, @name)) {
        return 'red';
    }
    elsif (grep(/(hypotheti)|(putative)|(probable)/i, @name)) {
        return 'orange';
    }
    elsif (grep(/(unknown)|(no annot)/i, @name)) {
        return 'yellow';
    }
    elsif (grep(/(express)/i, @name)) {
        return 'green';
    }
    else {
        return 'greenyellow';
    }
}

sub gene_fgcolor{
    my $feature = shift;
    my @name    = $feature->attributes('SubjectDescription');
    if (grep(/(transpos)|(repeat)|(repeti)/i, @name)) {
        return 'darkred';
    }
    elsif (grep(/(hypotheti)|(putative)|(probable)/i, @name)) {
        return 'orangered';
    }
    elsif (grep(/(unknown)|(no annot)/i, @name)) {
        return 'orange';
    }
    elsif (grep(/(express)/i, @name)) {
        return 'darkgreen';
    }
    else {
           return 'forestgreen';
    }
}

1;


Erick



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