#!perl
# This program reads a text file, collects usage statistics of strings of a fixed window size.

#input window size from command line
$windowSize = @ARGV[0]; 

#input name of the file to be read from command line
$infile = @ARGV[1];

#input name of the output file from command line
$outfile = @ARGV[2];

#remind user there is no window size or input file
if(!$windowSize or !$infile) {
  print "No window length or input file.\nUsage: perl my_perl.pl length infile outfile\n";
}


#read the input file if given
if($infile) {
  
  # open inputfile
  open(IN, $infile) or die "can not open $infile\n";

  #read the file
   while( $line =  ) {
  
     # join all the lines in the file
     $content .= $line; 
   }

  close(IN) or die "can not close $infile\n";

  # remove digits and blank spaces
  $content =~ s/[\s\d]//g;
  
  #change to uppercase
  $_ = $content;
  tr/a-z/A-Z/;
  $content = $_;

  # length of the sequence
  $_ = $content;
  $seqLength = tr/a-zA-Z//;
  
  # doing the statistics
  for($i=0; $i<$seqLength - $windowSize; $i++) {
    #sequence for a moving window of length $windowSize
    $winSeq = substr($content, $i, $windowSize);

    #put the sequence into unique categories using a Hashmap
    $stat{ $winSeq } ++;
  }

  # unique categories, also keys for the Hashmap
  @keys = keys(%stat);

  # order alphabetically
  @keys = sort(@keys);

  # printing out statistics
  #if output file name provided
  if($outfile) {
    open(OUT, ">$outfile") or die "can not open $outfile";
    for($i=0; $i<@keys; $i++) {
      print OUT "@keys[$i]\t$stat{@keys[$i]}\n";
    }
    close(OUT) or die "can not close $outfile";
  } 
  # else print to screen
  else {
    for($i=0; $i<@keys; $i++) {
      print "@keys[$i]\t$stat{@keys[$i]}\n";
    }
  }

}