\D{40}

open FILE, "~/test.gbk;" or die("could not open $input_file");

while (my $line = <FILE>) { 
    if ($line =~ [\d|\s]{8}\d \D{10} \D{10} \D{10} \D{10}) 
        push (@genome, $line)}

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

#!/usr/bin/perl -w 
use strict; 
use warnings; 
 
 
my @genome; 
my $input_file; 
my $line; 
my $output; 
my $genome; 
 
 
 
#$input_file = ~/test.gbk; 
open(my $fh, "<", "test.gbk") 
   or die "cannot open < test.gbk: $!"; 
 
while (my $line = <$fh>) { 
   if ($line =~ /[\d|\s]{8}\d \D{10} \D{10} \D{10} \D{10}/) { 
    push (@genome, $line); 
    } 
   } 
 
 
open(MYOUTFILE, ">-test.out")  or die("could not open test.out"); 
print MYOUTFILE "Start:End:angle"; 
 
 
# removes spaces from array  
$genome = @genome; 
$genome =~ s/\s|\d//g; 
# end of  
 
 
 
 
    while ($genome =~ /a+t?|t+/g) { 
         
       if ($+[0] - $-[0] == (4|7)) { 
            print MYOUTFILE "$-[0]:$+[0]:15/n"; 
       } 
       if ($+[0] - $-[0] == (5|6)) { 
            print MYOUTFILE "$-[0]:$+[0]:20/n"; 
       } 
     
 
}

ORIGIN       
        1 ttacaaataa gggactcggt caccccctga aacgcccaga ccgaaaaccc taaaccgaaa 
       61 cctaaaacct aaaaccctaa gcctaaacct agacctaaaa cctaaaaccc ccttaaaccc 
      121 ctaaacctaa acctaaacct aaacccctaa acctaggccc taaacctaaa cgccctaaac 
      181 ctaaaaccta aaacctgaaa cctaaaccta aaccctgaac ctaaaaaacc taaaacctaa

Start:End:angle 
5:8:15 
54:57:15 
etc. 
 
but at the moment the ouput just is  
Start:end:angle

$genome = @genome;

if ($+[0] - $-[0] == (4|7)) {

#!/usr/bin/perl  
use strict; 
use warnings; 
 
my $input_file; 
my $genome; 
 
#$input_file = ~/test.gbk; 
open( my $fh, "<", "test.gbk" ) 
  or die "cannot open < test.gbk: $!"; 
 
while ( my $line = <$fh> ) { 
    if ( $line =~ /[\d|\s]{8}\d \D{10} \D{10} \D{10} \D{10}/ ) { 
        $genome .= $line; 
    } 
} 
 
open( MYOUTFILE, ">-test.out" ) or die("could not open test.out"); 
print MYOUTFILE "Start:End:angle\n"; 
 
while ( $genome =~ /a+t?|t+/g ) { 
    my $offset = $+[0] - $-[0]; 
 
    if ( $offset == 4 or $offset == 7 ) { 
        print MYOUTFILE "$-[0]:$+[0]:15\n"; 
    } 
    elsif ( $offset == 5 or $offset == 6 ) { 
        print MYOUTFILE "$-[0]:$+[0]:20\n"; 
    } 
}

#!/usr/bin/perl -w 
use strict; 
use warnings; 
 
 
my @genome; 
my $input_file; 
my $line; 
my $output; 
my $genome; 
my $d; 
my $track; 
my $s; 
my $e; 
#$input_file = ~/test.gbk; 
open(my $fh, "<", "test.gbk") 
   or die "cannot open < test.gbk: $!"; 
 
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); 
 
    } 
   } 
 
 
open(MYOUTFILE, ">test.out")  or die("could not open test.out"); 
print MYOUTFILE "Start:End:Atract:angle\n"; 
 
 
# removes spaces from array  
$genome = "@genome"; 
$genome =~ s/\s|\d//g; 
# end of  
 
 
 
# prints output file/pushes data onto arrays 
    while ($genome =~ /a+t?|t+/g) { 
      $d = $+[0] - $-[0]; 
      $track = $&; 
      $s = $-[0]; 
      $e = $+[0]; 
 
        if ($d =~ m/4|7/) { 
            print MYOUTFILE "$s:$e:$track:15\n"; 
        } 
 
        if ($d =~ m/5|6/) { 
            print MYOUTFILE "$s:$e:$track:20\n"; 
        } 
     }

if ($d =~ m/4|7/) {

if ($d =~ m/^(4|7)$/) {

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

#!/usr/bin/perl -w  
use Math::Trig; 
use strict;  
use warnings; 
########set both start and end to 0 to scan full file########## 
my $start;   $start   = 0;  # starts scanning at  
my $end;     $end     = 0;  # ends scanning at  
my $bendmin; $bendmin = 45; # minimum bend 
my $Mtract;  $Mtract  = 99;  # maximum number of a-tracts in a scan 
my $ecut; 
my @genome;  
my $genome; 
my $length;  
my $Wi;my $X;my $Y; #for math 
my @X;my @Y; my @X1; my @Y1; my @X2; my @Y2; 
my $pop; 
my $k;my $ysum;my $xsum; 
 
#opens input 
open(my $fh, "<", "input.gbk")  or die "cannot open < test.gbk: $!";  
 
#Depricated output 
#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; 
 
#cuts the genome at the start and end points. 
$end -= 1; 
$start -= 1; 
my $size; $size = length($genome); 
$ecut = $size - $end; 
 
if ($ecut + $start < $size) { 
   if ($end > 0) {      
      $genome = reverse; 
      $genome =~ s/\w{$ecut}//; 
      $genome = reverse;} 
   if ($start > 0) { 
      $genome =~ s/\w{$start}//; 
   } else { $start = 0 ;} 
} 
 
 
 
# searches $genome, does math, prints output. 
while ($genome =~ /(?i)a+t?|(?i)t+/g) {  
   $length = $+[0] - $-[0];  
      if ( $length == 4 or $length == 5 or $length == 6 or $length == 7 ) {      
         $Wi = ((($-[0] + $start) + ($+[0] + $start)) / 3.18309886); #10.5 period  
         $Y = sin $Wi;  
         $X = cos $Wi; 
          
 
            if ( $length == 4 or $length == 7 ) {  
               $X *= 0.261799388; 
               $Y *= 0.261799388; 
            }  
  
            if ( $length == 5 or $length == 6 ) { 
               $X *= 0.34906585; 
               $Y *= 0.34906585; 
            }  
         $X = rad2deg($X); 
         $Y = rad2deg($Y); 
         push (@X, $X); 
         push (@Y, $Y); 
      }  
} 
 
#stores backups 
@X2 = @X;  
@Y2 = @Y; 
 
#sub add adds the a-tracts together untill they have reached the max number of a-tracts in a curve 
#it prints when the curve is larger then the bend min 
sub add {   
   $pop = shift (@X); 
   push(@X1, $pop); 
   $pop = shift (@Y); 
   push(@Y1, $pop); 
   $k = 0; 
   my $n; $n = 0; 
 
 
   while ( $n + 1 < $Mtract ) { 
      $pop = shift (@X); 
      push(@X1, $pop); 
      $xsum = 0; 
      foreach (@X1) { 
      $xsum += $_;} 
      $xsum *= $xsum; 
 
 
      $pop = shift (@Y); 
      push(@Y1, $pop);    
      $ysum = 0; 
      foreach (@Y1) { 
      $ysum += $_;} 
      $ysum *= $ysum; 
      $k = sqrt ($xsum + $ysum);   
      $n += 1; 
       
      if ( $k <= $bendmin ) { 
         print "degrees: $k\n"; 
      } 
   } 
 
 
#this bit is so that if i run &add multiple times (which my end result will) it will advance 
   shift(@X1); 
   shift(@Y1); 
 
   while ($n > 0) { 
      $pop = pop(@X1); 
      unshift (@X, $pop); 
      $pop = pop(@Y1); 
      unshift (@Y, $pop); 
      $n -= 1; 
   } 
} 
 
&add;

while (my $line = <$fh>) {  
 
    next if $line =~ /^\s*$/;  
 

  
 
do{  
 
    open( my $fh, "<", "input.gbk" ) or die "cannot open < test.gbk: $!";  
 
    $INPUT_RECORD_SEPARATOR =  undef;  
 
    $genome = <$fh>;  
 
    close $fh;  
 
};  
 
$genome =~ s/[^agct]//g;