#
#
# The directives below enforce variable declarations and ensure your program
# will be parsed to provide more feedback about possible syntax and logical errors.
#

use strict;                # enforce variable declarations
use warnings;              # enable warnings

#
# Declare/initialize all variables used in main program body.
#

my ($A_count)       = 0;     # number of 'a' or 'A' in user-supplied sequence
my ($base)          = '';    # an extracted letter from the sequence
my ($C_count)       = 0;     # number of 'c' or 'C' in user-supplied sequence
my ($filename)      = '';    # the name of the file containing the input sequence(s)
my (@filesequences) = ();    # array containing lines read from input file
my ($G_count)       = 0;     # number of 'g' or 'G' in user-supplied sequence
my ($i)             = 0;     # used to index into array of sequences
my ($line_count)    = 0;     # number of lines read from input file
my ($option)        = 0;     # the user's selected menu option
my ($position)      = 0;     # the current position within the sequence
my ($sequence)      = '';    # the DNA sequence to be processed
my ($T_count)       = 0;     # number of 't' or 'T' in user-supplied sequence

#
# Display welcome message and program explanation.
#

print "\n *****************************************************";
print "\n **                                                 **";
print "\n **       Nucleotide Counter, version 2.0           **";
print "\n **                                                 **";
print "\n **         Written by J.M Wagner 2014              **";
print "\n **                                                 **";
print "\n *****************************************************";
print "\n *                                                   *";
print "\n *  This program will count the number of different  *";
print "\n *  nucleotides present in the sequence you provide. *";
print "\n *  Both uppercase and lowercase abbreviations will  *";
print "\n *  be counted. Input can be provided at the         *";                         
print "\n *  keyboard or can be read from a file.             *";
print "\n *                                                   *";
print "\n *                                                   *";
print "\n *****************************************************";

print "\n\n\t Program options:";
print "\n\t -----------------------------";
print "\n\t 1. Enter sequence at keyboard";
print "\n\t 2. Read input sequences from a file";
print "\n\t 3. Exit";

print "\n\n Please enter your menu option>";
$option = <STDIN>;

#
# Confirm that user has entered a valid menu option.
#
while (($option < 1) or ($option > 3))
  {
  chomp $option;
  print "\n ERROR: The value $option is not a valid menu option.";
  print "\n\n Please enter your menu option>";
  $option = <STDIN>;
  } # end while

#
# Obtain input DNA sequence from user.
#


# **************************************************************************
# OPTION 1 - Obtain and process input sentence provided at keyboard.
# **************************************************************************

if ($option == 1)
  {

#
# Obtain input DNA sequence from user.
#
print "\n\n Please enter the DNA Sequence to be processed";
print "\n >";

$sequence = <STDIN>;
print "\n Processed DNA sequence:   $sequence";

#
# Count the number of nucleotides by processing the sequence of characters
# one character at a time.
#

for ($position = 0; $position < length($sequence); ++$position)
  {
  $base = substr($sequence, $position, 1);


  if (($base eq 'a') or ($base eq 'A') or 
      ($base eq 'c') or ($base eq 'C') or
      ($base eq 'g') or ($base eq 'G') or
      ($base eq 't') or ($base eq 'T')) 
    {

    if (($base eq 'a') or ($base eq 'A'))
      {
      ++$A_count;
      } # end if

    if (($base eq 'c') or ($base eq 'C'))
      {
      ++$C_count;
      } # end if

    if (($base eq 'g') or ($base eq 'G'))
      {
      ++$G_count;
      } # end if
       
    if (($base eq 't') or ($base eq 'T'))
      {
      ++$T_count;
      } # end if


    } # end if
   } # end for
#
# Display final results.
#
print "\n Number of A nucleotides:   $A_count";
print "\n Number of C nucleotides:   $C_count";
print "\n Number of G nucleotides:   $G_count";
print "\n Number of T nucleotides:   $T_count";

print "\n\n Program completed successfully.\n";
  
  }end if

# **************************************************************************
# OPTION 2 - Obtain and process input sentences provided in user file.
# **************************************************************************

elsif ($option == 2)
  {  
#
# Read input sequence(s) from file provided by user.
#
print "\n\n Please enter the filename>";
$filename = <STDIN>;
  
unless(open(SEQUENCEFILE, $filename))
   {
   print "\n\t --> ERROR: Cannot open file: $filename";
   exit;
   }

@filesequences = <SEQUENCEFILE>;
close(SEQUENCEFILE);

$line_count = @filesequences;
print "\n\t --> NOTE: File opened -- $line_count lines of text read.\n";

# print @filesequences;

#
# Count the number of nucleotides by processing the sequence of characters
# one sequence at a time.
#

for ($i = 0; $i < $line_count; ++$i)
   {

#
# Initialize $sequence to the next line of text from file.
#

$sequence = $filesequences[$i];
print "\n    $i. Processed sequence:      $sequence";

#
# Count the number of nucleotides in the current sequence.
#

   $position = 0;
   while ($position < length($sequence))
     {
     $base = substr($sequence, $position, 1);

     if (($base eq 'a') or ($base eq 'A') or 
         ($base eq 'c') or ($base eq 'C') or
         ($base eq 'g') or ($base eq 'G') or
         ($base eq 't') or ($base eq 'T')) 
       {

       if (($base eq 'a') or ($base eq 'A'))
       {
       ++$A_count;
       } # end if

       if (($base eq 'c') or ($base eq 'C'))
       {
       ++$C_count;
       } # end if

       if (($base eq 'g') or ($base eq 'G'))
       {
       ++$G_count;
       } # end if
       
       if (($base eq 't') or ($base eq 'T'))
       {
       ++$T_count;
       } # end if
     
     ++$position; 
     } # end while
    } # end for

print "\n Number of A nucleotides:   $A_count";
print "\n Number of C nucleotides:   $C_count";
print "\n Number of G nucleotides:   $G_count";
print "\n Number of T nucleotides:   $T_count";
 
print "\n\n Program completed successfully.\n";
   } # end elsif

#
# **************************************************************************
# Write final results to default output file.
# **************************************************************************

$filename = "results.dat";

unless(open(OUTFILE, ">$filename"))
  {
  print "\n\t --> ERROR: Cannot open file: $filename";
  exit;
  }
print "\n\n\t --> NOTE: File opened for writing: $filename\n";

print OUTFILE "\n Total number of Adenine:     $A_count";
print OUTFILE "\n Total number of Cytosine:    $C_count";
print OUTFILE "\n Total number of Guanine:     $G_count";
print OUTFILE "\n Total number of Thymine:     $T_count";
close(OUTFILE);

print "\n\n Program completed successfully.\n";
exit;