#!/usr/bin/perl -w

use strict;

my $numArgs = $#ARGV + 1;  # calculate number of arguments passed to program from command line
my $inputfile;
my $inputfile2;
my $outputfile;  # initialise filename variables
my $reqdcolumn;

if ($numArgs < 1) {
	die "Please choose a column to append";
}

elsif ($numArgs >= 4) {
	
	$inputfile = "$ARGV[1]";
	print "Input filename1 received from command line.  Opening '$inputfile'...\n";
	
	$inputfile2 = "$ARGV[2]";
	print "Input filename2 received from command line.  Opening '$inputfile2'...\n";
	
	$outputfile = "$ARGV[3]";
	print "Output filename received from command line.  Opening '$outputfile'...\n";
	
	$reqdcolumn = $ARGV[0];
	print "Required column received from command line.  Appending column $reqdcolumn of '$inputfile' to '$inputfile2'...\n";

}

elsif ($numArgs == 3) {

	$inputfile = "$ARGV[1]";
	print "Input filename1 received from command line.  Opening '$inputfile'...\n";
	
	$inputfile2 = "$ARGV[2]";
	print "Input filename2 received from command line.  Opening '$inputfile2'...\n";
	
	$reqdcolumn = $ARGV[0];
	print "Required column received from command line.  Appending column $reqdcolumn of '$inputfile' to '$inputfile2'...\n";
	
	print "Please enter the path of your output file: ";
	chomp($outputfile = <STDIN>);
}

elsif ($numArgs == 2) {

	$inputfile = "$ARGV[1]";
	print "Input filename1 received from command line.  Opening '$inputfile'...\n";

	print "Please enter the path of your second input file: ";
	chomp($inputfile = <STDIN>);
	
	$reqdcolumn = $ARGV[0];
	print "Required column received from command line.  Appending column $reqdcolumn of '$inputfile' to '$inputfile2'...\n";
	
	print "Please enter the path of your output file: ";
	chomp($outputfile = <STDIN>);

}	

elsif ($numArgs == 1) {

	print "Please enter the path of your first input file: ";
	chomp($inputfile = <STDIN>);

	print "Please enter the path of your second input file: ";
	chomp($inputfile = <STDIN>);
	
	$reqdcolumn = $ARGV[0];
	print "Required column received from command line.  Appending column $reqdcolumn of '$inputfile' to '$inputfile2'...\n";
	
	print "Please enter the path of your output file: ";
	chomp($outputfile = <STDIN>);
}	

else {

	print "Please enter the path of your first input file: ";
	chomp($inputfile = <STDIN>);

	print "Please enter the path of your second input file: ";
	chomp($inputfile = <STDIN>);

	print "Please choose the number of the column in inputfile1 to append to inputfile2 (first column is zero): ";
	chomp($reqdcolumn = <STDIN>);
	
	print "Please enter the path of your output file: ";
	chomp($outputfile = <STDIN>);
}

open INPUTFILE, "<$inputfile" || die "An error occured whilst opening your input file '$inputfile': $!";

open OUTPUTFILE, ">$outputfile" || die "An error occured whilst creating your output file '$outputfile': $!";


print "INPUT: $inputfile\n";
print "OUTPUT: $outputfile\n";  #display input and output file names

my @fields;
my $fields;
my @selectedcolumn;
my $selectedcolumn;
my $lineindex = 0;

while(defined(my $line = <INPUTFILE>)) {  # read through each line in turn while they still exist 
		
		$line =~ s/[\n]+//g;  # remove new line characters
		@fields = split(/,\t*/, $line);  # split line into fields according to comma delimiter
		
		$selectedcolumn[$lineindex] = $fields[$reqdcolumn];
		
		$lineindex++;
}	

$lineindex = 0;
close INPUTFILE;
open INPUTFILE, "<$inputfile2" || die "An error occured whilst opening your input file '$inputfile': $!";

while(defined(my $line = <INPUTFILE>)) {  # read through each line in turn while they still exist 
		
		$line =~ s/[\n]+//g;  # remove new line characters
		
		my $newcolumn = $selectedcolumn[$lineindex];

		print OUTPUTFILE "$line,$newcolumn\n";
		
		$lineindex++;
}	


close INPUTFILE;
close OUTPUTFILE;  # close input and output files