use DrawTransmembrane;

Can't locate DrawTransmembrane.pm

##</code><code>##

Warning: Cannot install DrawTransmembrane, don't know what it is.
Try the command

    i /DrawTransmembrane/

to find objects with matching identifiers.

##</code><code>##

Global symbol "$topology_final" requires explicit package name at DrawTransmembrane.pl line 6.
Global symbol "@total_top" requires explicit package name at DrawTransmembrane.pl line 8.
Global symbol "$topology_final" requires explicit package name at DrawTransmembrane.pl line 9.
Global symbol "$topology_final" requires explicit package name at DrawTransmembrane.pl line 11.
Global symbol "@total_top" requires explicit package name at DrawTransmembrane.pl line 18.
Global symbol "@total_top" requires explicit package name at DrawTransmembrane.pl line 19.
Global symbol "@total_top" requires explicit package name at DrawTransmembrane.pl line 28.
Execution of DrawTransmembrane.pl aborted due to compilation errors.

##</code><code>##

Can't locate object method "new" via package "DrawTransmembrane" (perhaps you forgot to load "DrawTransmembrane"?)

##</code><code>##

Not a HASH reference at /usr/share/perl5/Bio/Graphics/DrawTransmembrane.pm line 125.

##</code><code>##

#!/usr/bin/perl
use strict;
use warnings;
#use DrawTransmembrane;
use Bio::Graphics::DrawTransmembrane;

my $topology_final = 'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII0IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIMMMMMMMMMOOOOOOOOOOOOOOOMMMMMMMIIIMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIIIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIIIMMMMMMMMMOOOOOOOMMMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIIMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOMMMMMMMMMMMIIIIIMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMM';

my @total_top = ();
if($topology_final=~/M/) {
    while ($topology_final =~/(.)\1*/g) {
	if ($1 eq "M") {
	    my $start_TM = $-[0] + 1;
	    my $end_TM = $+[0];
	    
	    push @total_top, $start_TM;
	    push @total_top, $end_TM;
	}
    }
    
    #my $image = DrawTransmembrane->new( -title=>"topology prediction image",
    my $image = Bio::Graphics::DrawTransmembrane->new( -title=>"topology prediction image",
						       -n_terminal=>'in',
						       -topology=>\@total_top,
						       -bold_helices=> 1,
						       -bold_labels=>1,
						       -text_offset=>-25,
						       -helix_label=>'b',
						       -outside_label=>'Extracellular',
						       -inside_label=>'Periplasm',
						       -membrane_label=>'Membrane',
						       -helix_width=>30,
						       -vertical_padding=>150,
						       -horizontal_padding=>120,
						       -n_terminal_offset=>50,
						       -n_terminal_height=>220,
						       -c_terminal_offset=>30,
						       -c_terminal_height=>220,
						       -helix_label=>'Sheet',
						       -colour_scheme=>'yellow'	);	

    open (OUTPUT, '>', 'test.png');
    binmode OUTPUT;
    print OUTPUT $image->png; 
    close (OUTPUT);
}

##</code><code>##

#!/usr/bin/perl
use strict;
use warnings;
use Bio::Graphics::DrawTransmembrane;

## Simple use - -topology is the only option that is required
my @topology = (20,45,59,70,86,109,145,168,194,220);

## More advanced use
my %labels = ( 5 => '5 - Sulphation Site',
	       21 => '1st Helix',
	       47 => '40 - Mutation',
	       60 => 'Voltage Sensor',
	       72 => '72 - Mutation 2',
	       73 => '73 - Mutation 3',
	       138 => '138 - Glycosylation Site',
	       170 => '170 - Phosphorylation Site',
	       200 => 'Last Helix' );

my $im = Bio::Graphics::DrawTransmembrane->new( 
    -title => 'This is a cartoon displaying transmembrane helices.',
    -n_terminal=> 'out',
    -bold_helices=> 1,
    -labels=> \%labels,
    -text_offset=> -15,
    -outside_label=>'Lumen',
    -inside_label=>'Cytoplasm',
    -membrane_label=>'Membrane',
    -vertical_padding=> 155,
    -topology => \@topology,
    -bold_helices=> 1,
    );

## Now write the image to a *.png file
open(OUTPUT, ">output.png");
binmode OUTPUT;
print OUTPUT $im->png;
close OUTPUT;

##</code><code>##

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
use Bio::Graphics::DrawTransmembrane;

my $topology_final = 'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII0IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIMMMMMMMMMOOOOOOOOOOOOOOOMMMMMMMIIIMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIIIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIIIMMMMMMMMMOOOOOOOMMMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIIMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOMMMMMMMMMMMIIIIIMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMM';

my @total_top = ();
if($topology_final=~/M/) {
    while ($topology_final =~/(.)\1*/g) {
	if ($1 eq "M") {
	    my $start_TM = $-[0] + 1;
	    my $end_TM = $+[0];
	    
	    push @total_top, $start_TM;
	    push @total_top, $end_TM;
	}
    }
}

print Dumper(\@total_top);

## More advanced use
my %labels = ( 176 => '5 - Sulphation Site',
	       206 => '1st Helix',
	       256 => '40 - Mutation',
	       276 => 'Voltage Sensor',
	       316 => '72 - Mutation 2',
	       392 => '73 - Mutation 3',
	       489 => '138 - Glycosylation Site',
	       539 => '170 - Phosphorylation Site',
	       747 => 'Last Helix' );

my $image = Bio::Graphics::DrawTransmembrane->new( 
    -title=>"topology prediction image",
    -n_terminal=>'in',
    -topology=>\@total_top,
    -bold_helices=> 1,
    -labels=> \%labels,
    -bold_labels => 1,
    -text_offset=>-25,
    -helix_label=>'b',
    -outside_label=>'Extracellular',
    -inside_label=>'Periplasm',
    -membrane_label=>'Membrane',
    -helix_width=>30,
    -vertical_padding=>150,
    -horizontal_padding=>120,
    -n_terminal_offset=>50,
    -n_terminal_height=>220,
    -c_terminal_offset=>30,
    -c_terminal_height=>220,
    -helix_label=>'Sheet',
    -colour_scheme=>'yellow');    

open (OUTPUT, '>', 'test.png');
binmode OUTPUT;
print OUTPUT $image->png; 
close (OUTPUT);