#!/usr/bin/perl

# -----------------------------------------------------------------------
# replaceX.pl 1.0
#
# This programm replace character A with B from an input textfile 
# and writes the result to an output textfile.
#  
# For example it is possible to replace all A,C,T,G with the value '1'
# and all X and N with value '0'.
#
# The command line for this is:
# ./replaceX.ps input.txt output.txt 'X|N' 0 'A|C|T|G' 1
#
#
#  Copyright by Joern Hameister (2005)
# -----------------------------------------------------------------------

if(@ARGV<4) {
	print "This programm replace character A with B from an input textfile and writes the result to an output textfile.\nParameter 1: Inputfile\nParameter 2: Outputfile\nParameter 3: Character A\nParameter 4: Character B\nFor example: ./replaceX.pl ./inputfile.txt ./outputfile.txt A B\nRegular expressions in the parameters are possible too.\nExample: ./replaceX.pl ./inputfile.txt ./outputfile.txt X 0 'A|C|T|G' 1\nThis command replace all X with 0 and all A or C or T or G with 1.";
}
elsif(@ARGV%2==1) {
	print "Number of parameters must be odd.\n";
}
else {
	print "Read from @ARGV[0] (Inputfile)\n";
  print "Write to @ARGV[1] (Outputfile)\n";

	open(INPUT , "<", @ARGV[0]);
	open(SINK , ">" , @ARGV[1]);
	
	while(<INPUT>) {
		for($i= 2; $i < @ARGV;) {
			$char1 = @ARGV[$i];
		  $char2 = @ARGV[$i+1];
		  $i += 2;
		  # print "Replace $char1 with $char2\n";
				
			s/$char1/$char2/g;
		}	
		print SINK $_;
	}
}