bin/bp_chaos_plot

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