#!/usr/bin/perl

my $organism;

if ($#ARGV == 0){
	$organism = $ARGV[0];
}
else{
	print "Wrong number of arguments\nUSAGE: genomeAtlasCf.pl <organismName>";
}

open LENGTH, "${organism}.length" or die;
my @l_lines = <LENGTH>;
my $length = $l_lines[0];
chomp $length;
close LENGTH;

open LENGHTTEXT, "${organism}.lengthtext" or die;
my @t_lines = <LENGHTTEXT>;
my $lengthtext = $t_lines[0];
chomp $lengthtext;
close LENGTHTEXT;

open STRIPQ, "${organism}.organismStripQuote" or die;
my @s_lines = <STRIPQ>;
my $name = $s_lines[0];
chomp $name;
close STRIPQ;

open (MYFILE, "> ${organism}.genomeatlas.cf");
printf MYFILE ("genomesize 5810058;
stamp \"GENOME ATLAS\";
noatlas;
noatlasscore;
ann CDS pos 0.0 0.0 1.0 \"CDS +\" fillarrow mark;
ann CDS neg 1.0 0.0 0.0 \"CDS -\" fillarrow mark;
ann rRNA 0.0 1.0 1.0 \"rRNA\" fillarrow mark;
ann rRNA pos 0.0 1.0 1.0 \"rRNA +\" fillarrow mark;
ann rRNA neg 0.0 1.0 1.0 \"rRNA -\" fillarrow mark;
ann tRNA 0.0 1.0 0.0 \"tRNA\" fillarrow mark;
ann tRNA pos 0.0 1.0 0.0 \"tRNA +\" fillarrow mark;
ann tRNA neg 0.0 1.0 0.0 \"tRNA -\" fillarrow mark;
dat $organism.curvature.gz 1 0.0 0.0 0.0 \"Intrinsic Curvature\" boxfilter %d;
dat $organism.ornstein.gz 1 0.0 0.0 0.0 \"Stacking Energy\" boxfilter %d;
dat $organism.travers.gz 1 0.0 0.0 0.0 \"Position Preference\" boxfilter %d;
dat $organism.blastDirect.genomemap0.gz 1 0.0 0.0 0.0 \"Global Direct Repeats\";
dat $organism.blastInverted.genomemap0.gz 1 0.0 0.0 0.0 \"Global Inverted Repeats\";
dat $organism.baseskews.col.gz 3 0.0 0.0 0.0 \"GC Skew\" boxfilter %d;
dat $organism.baseskews.col.gz 4 0.0 0.0 0.0 \"Percent AT\" boxfilter %d;
circletics auto;
circletext \"$name\" \"$lengthtext bp\";
circle $organism.baseskews.col.gz 4 \"001010_101010_100000.cm2\" by 0.2 0.8;
circle $organism.baseskews.col.gz 3 \"100010_101010_001010.cm2\" by avg 3.0 dev;
circle $organism.blastInverted.genomemap0.gz 1 \"101010_100000.cm2\" by 5.0 7.5;
circle $organism.blastDirect.genomemap0.gz 1 \"101010_000010.cm2\" by 5.0 7.5;
circle CDS pos, CDS neg, rRNA, tRNA by dir;
circle $organism.travers.gz 1 \"001000_101010_100010.cm2\" by avg 3.0 dev;
circle $organism.ornstein.gz 1 \"001000_101010_100000.cm2\" by avg 3.0 dev;
circle $organism.curvature.gz 1 \"100600_101010_000010.cm2\" by avg 3.0 dev;
file $organism.curvature.gz dat;
file $organism.ornstein.gz dat;
file $organism.travers.gz dat;
file $organism.ann ann;
file $organism.blastDirect.genomemap0.gz dat;
file $organism.blastInverted.genomemap0.gz dat;
file $organism.baseskews.col.gz dat;
"), ((0.002*$length), (0.002*$length), (0.002*$length), (0.001*$length), (0.001*$length));

close MYFILE;