/usr/bin/bp_chaos_plot is in bioperl 1.7.2-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 | #!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
use Getopt::Long;
use GD;
use vars qw( $USAGE %VALIDFORMATS);
%VALIDFORMATS = ( 'png' => 1,
'jpeg' => 1,
'gd2' => 1,
'gd' => 1,
'gif' => 1,
'wbmp' => 1 );
$USAGE = "usage:\tchaos_plot -i/--input=INPUTFILE -f/--format=SEQFORMAT \n".
"\t-o/--output=OUTPUTFILE -g/--graphics=GRAPHIC TYPE\n".
"\t-w/--width=600 -h/--height=400\n";
$USAGE .= "\tValid graphics formats: (" . join(",", ( keys %VALIDFORMATS )) .")\n";
$USAGE .= "\tImage size defaults to 600x400, SEQFORMAT to fasta\n";
$USAGE .= "\tINPUTFILE can also be read from STDIN\n";
my ($format,$graph,$width,$height,$seqfile,$output) = ('fasta', 'png', 600, 400);
GetOptions( "i|input:s" => \$seqfile,
"f|format:s" => \$format,
"o|output:s" => \$output,
"g|graph|graphics:s" => \$graph,
"width:i" => \$width,
"height:i" => \$height
);
if( ! $output || ! $VALIDFORMATS{$graph} ) {
die $USAGE ;
}
my $seqin;
$seqfile = shift unless $seqfile;
if( defined $seqfile ) {
print "Could not open file [$seqfile]\n$USAGE" and exit unless -e $seqfile;
$seqin = new Bio::SeqIO(-format => $format,
-file => $seqfile);
} else {
$seqin = new Bio::SeqIO(-format => $format,
-fh => \*STDIN);
}
my $img = new GD::Image($width,$height);
my $white = $img->colorAllocate(255,255,255);
my $black = $img->colorAllocate(0,0,0);
my $seq = $seqin->next_seq;
die("Sequence type must be DNA not " . $seq->alphabet())
unless $seq->alphabet ne 'dna' or $seq->alphabet ne 'rna';
my %nmerdata;
my $len = $seq->length();
my $max = 0;
my ($x,$y) = ( 0.5, 0.5);
$img->string(gdGiantFont, 1,1, 'A', $black);
$img->string(gdGiantFont, 0,$height - 15, 'C', $black);
$img->string(gdGiantFont, $width - 15,1, 'T', $black);
$img->string(gdGiantFont, $width - 15,$height -20, 'G', $black);
for( my $i = 1; $i <= $len; $i++ ) {
my $base = lc $seq->subseq($i,$i);
if( $base eq 'a' ) {
$x *= 0.5;
$y *= 0.5;
} elsif ( $base eq 'g' ) {
$x = ( $x + 1.0 ) * 0.5;
$y = ( $y + 1.0 ) * 0.5;
} elsif ( $base eq 'c' ) {
$x *= 0.5;
$y = ( $y + 1.0 ) * 0.5;
} elsif ( $base eq 't' or $base eq 'u' ) {
$x = ( $x + 1.0 ) * 0.5;
$y *= 0.5;
}
$img->setPixel($x * $width,$y * $height, $black);
}
open my $OUT, '>', $output or die "Could not write file '$output': $!\n";
binmode $OUT;
$graph =~ s/jpg/jpeg/;
print $OUT $img->$graph();
close $OUT;
__END__
=head1 NAME
bp_chaos_plot - a chaos plot from DNA and RNA sequences
=head1 SYNOPSIS
bp_chaos_plot.pl -i/--input=INPUTFILE -f/--format=SEQFORMAT
-o/--output=OUTPUTFILE -g/--graphics=GRAPHIC FORMAT
-w/--width=WIGHT -h/--height=HEIGHT
=head1 DESCRIPTION
This scripts generates image files using GD image library to visualize
nucleotide sequences using chaos plot.
=head1 OPTIONS
Valid graphics formats are currently gd, gd2, png, wbmp, jpeg and gif.
The default size of the image file is 600x400.
The sequence input can be provided using any of the three methods:
=over 3
=item unnamed argument
bp_chaos_plot filename
=item named argument
bp_chaos_plot -i filename
=item standard input
bp_chaos_plot < filename
=back
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
=head1 HISTORY
This code is based on EMBOSS C code for chaos.c by Ian Longden.
Included are documentation from EMBOSS code:
Chaos produces a chaos plot. The original application is part of the
ACEDB genome database package, written by ** Richard Durbin (MRC LMB,
UK) rd@mrc-lmba.cam.ac.uk, and Jean Thierry-Mieg (CRBM du CNRS,
France) mieg@crbm1.cnusc.fr
=cut
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