I am sure I am overthinking this. I have been working on it for 5days now and cant seem to get it to work. The code is supposed to check if 2 DNA sequences given as a user input are reverse complements to each other. Can you tell me where I am going wrong/suggestions?

 
use warnings;
use strict;
 
#Check if there is an input of sequences
if((scalar @ARGV)==0){
  print "Please enter two sequences as arguments on the command line";
  exit;
}
 
#get the input from command line
my @two_seq=@ARGV;
my $sequence=join('',@two_seq);
 
#Remove newline and/or blank space between sequences
chomp $sequence;
$sequence=~s/^\n*$//g;
$sequence=~tr/atcg/ATCG/;
 
 
#Check if there are only two sequences entered
if((scalar @two_seq)>2){
  print "Sorry,no more than two sequences please.\nNote:Use space to s
+eperate two sequences.\n";
  exit;
}
 
#Check if two sequences are of the same length
if((length $two_seq[0])!=(length $two_seq[1])){
  print "Sorry, the two sequences you have just entered are of differe
+nt lengths.\nPlease try again on the command line.";
  exit;
}
 
#Initialize joined sequences to be checked
my @check_seq=split('',$sequence);
 
#Compare reverse complement sequences
for(my $i=0;$i<(length $sequence)/2;$i++)
{
  #Start checking from both end of the sequence
  my $start_base=shift @check_seq;
  my $end_base=pop @check_seq;
  $end_base=~tr/ATCG/TAGC/;
  if($start_base eq $end_base){
    next;
  }else{
    print "Unfortunately, the two sequences are not reverse-complement
+.\n";
    exit;
  }
}
 
#W reverse-complements
print "Yes, the two sequences are reverse-complement of each other.\n"
+;
exit;

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In reply to Reverse Complement by stamp1982

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