#!/usr/bin/perl -w 

use strict; 

use warnings; 

my @genome; 

my $genome;

my $length; 

my $Wi;my $X;my $Y; #for math



#opens input

open(my $fh, "<", "input.gbk")  or die "cannot open < test.gbk: $!"; 

#opens output and prints header

open(MYOUTFILE, ">test.out")  or die "could not open test.out"; 

print MYOUTFILE "Start:End:A-tract:Xi:Yi:Angle\n"; 



#imports file removes spaces and digits 

while (my $line = <$fh>) { 

   if ($line =~ /[\d|\s]{8}\d\s\D{10}\s\D{10}\s\D{10}\s\D{10}/) { 

      push (@genome, $line);  

   } 

} 

$genome = "@genome"; 

$genome =~ s/\s|\d//g;



# searches $genome, does math, prints output.

while ($genome =~ /a+t?|t+/g) { 

   $length = $+[0] - $-[0]; 

      if ( $length == 4 or $length == 5 or $length == 6 or $length == 7 ) {     

         $Wi = (((($-[0] + $+[0]) / 2) / 10) * 6.28318531);

         $Y = sin $Wi; 

         $X = cos $Wi;

         print MYOUTFILE "$-[0]:$+[0]:$&:$X:$Y:";



            if ( $length == 4 or $length == 7 ) { 

               print MYOUTFILE "15\n"; 

            } 

 

            if ( $length == 5 or $length == 6 ) {

               print MYOUTFILE "20\n"; 

            } 

      }

}