Hi fellow Monks!
I would like to ask you to help me write the following code in a more "sophisticated" way.
What the code does is, given to strings of characters, like the following 
$string1 = "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIIMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIIMMMMMMMMMMM
+MMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOO
+OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMIIIIIMMMMMMMM
+MMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIMMMMMMMMMOOOOOOOOOO
+OOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIMMMMMMMMMOOOOOOOOOOOOOOOOOOOMMM
+MMMMMMIIIIIIIIIIIIIIIIIIIIIIIIIIIMMMMMMMMOMMMMMMMMMMMMM";

$string2 = "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+IIIIIIIIIMMMMMMMMMMMMOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMMIIIIIMMMMMMMMMM
+MMMOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMIIIMMMMMMMMMMMMMMOOOOOOOOOO
+OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMIIIMMMMMMMMMM
+MMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMIIIMMMMMMMMMMMMMMMOOOO
+OOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMIIIMMMMMMMMMMMMOOOOOOOOOOOOOOOMMMM
+MMMMMMIIIIIIMMMMMMMMMMMMOOOOOOOOOOOOOOOOOMMMMMMMMMMMMII";

[download]

the program should check the following:
1. Do both strings start with the same character? (in this case yes, they do)
2. Do both strings contain the same number of M substrings? (In this case yes, because both have 13).
3.Do each pair of the M substrings overlap for at least 5 positions (we would compare the 1st M substring of the first string to the 1st M substring of the seecond string and so on).
My code is the following, please bear with me because I am kind of new in Perl:
#N-terminal
$Nterm_topo=substr($string2,0,1);
$Nterm_pred=substr($string1,0,1);

#TM number and orientation for $string2
$TM_topo=0;
$all_tms='';
while($string2=~/M+/g)
{
$TM_topo++;
$start_tm=$-[0]; 
$end_tm=$+[0]-1;
                $all_tms.=$start_tm."-".$end_tm."#";
}
chop $all_tms;

#TM number and orientation for $string1
$TM_pred=0;
while($string1=~/(M+)/g) { $TM_pred++; }    

################ Orientation ############################
$correct_TM_location=0;
@split_tms_real=split(/#/, $all_tms);

for ($i=0;$i<=$#split_tms_real;$i++)
{
$corresp_TM_real=$split_tms_real[$i];
if($corresp_TM_real=~/(\d+)\-(\d+)/) 
  { 
     $start_real=$1; $end_real=$2;
     $real_length=$end_real-$start_real+1;
     $substr_pred=substr($string1,$start_real, $real_length);
                    $count_M=$substr_pred=~tr/M//;

if($count_M>=5) {$correct_TM_location++;}
                }                    
}                

if( $Nterm_topo eq $Nterm_pred  $TM_topo==$TM_pred && $TM_pred==$corre
+ct_TM_location) 
{
   $correct_topo++; 
}

[download]

In reply to Can you help me re-write this code? by Anonymous Monk

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