Here is all my code, warning on first if line.

!/usr/bin/perl -w


use strict;


open(INFILE,"<$ARGV[0]") or die "can't open $ARGV[0]";
open(OUTFILE,">$ARGV[1]") or die "can't open $ARGV[1]";


my @result   = split '', 'abcdefghijklmno';
my @arg1   = (0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15);
my %rules;


# Build the rules hash
    $rules{$arg1[$_]} = $result[$_] for 0 .. $#result;

my $run = 0;
my @bin = ();
my @newseq = ();

while ( <INFILE> ) {
   chomp;
   @bin= split(//, $_);
   for my $i (0..$#bin) {
      if ($bin[$i]==0){
         $run=0;
         push @newseq,$run;
      }
      elsif ($bin[$i]==1 && $bin[$i+1]==0||$bin[$i+1]==0)){
         $run++;
         push @newseq, $run;
      }
      else {
         $run++;
      }
   }
}
my $m = $#newseq+1;

 for (1 .. $m) {
       if ( $_ % 80 != 0){ print OUTFILE "$rules{$newseq[$_-1]}"}
          else{  print OUTFILE "$rules{$newseq[$_-1]}\n"; }
}
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