#! /usr/bin/perl

use strict;

##This program concatenates the output files together and creates an option file for scoring.

print "Enter the base name of the output files: ";
my $outFile = <STDIN>;
chomp ($outFile);

print "Enter the number of nodes used: ";
my $nodes = <STDIN>;
chomp ($nodes);

print "Enter the csfasta file name: ";
my $inputFile1 = <STDIN>;
chomp ($inputFile1);
if (not (-e "$inputFile1"))
{
	print "File does not exist. Exiting program\n";
	exit;
}

print "Enter the reference genome file name: ";
my $ref = <STDIN>;
chomp ($ref);
print "Enter the RAM available: ";
my $reads = <STDIN>;
chomp ($reads);

print "Combining binary files...\n";

if (-e ($outFile."1".".best"))
{
	cat ($outFile, ".best");
}

print "Combining text files...\n";

if (-e ($outFile."1".".best.txt"))
{
	cat ($outFile, ".best.txt");
}

open (INPUT, ">scoring.pref");

print INPUT "$ref\n";
print INPUT "$inputFile1\n";
print INPUT "Qual.qual\n";
print INPUT "$outFile\n";
print INPUT "0\n";
print INPUT "$reads\n";
print INPUT "0\n";
print INPUT "false\n";
print INPUT "true\n";
print INPUT "-1\n";

print "To score, run: [socs] scoring.pref --score\n";

sub cat
{
	my $outFile = shift;
	my $ext = shift;
	my $out = $outFile.$ext;
	open (OUT, ">$out");
	my $i;
	my $file;
	my $line;

	for ($i = 1; $i <= $nodes; $i++)
	{
		$file = $outFile.$i.$ext;
		print $file, "\n";
		if (-e "$file")
		{
			open (INPUT, "$file");
			while (defined ($line = <INPUT>))
			{
				print OUT $line;
			}
			print OUT "\n";
			close INPUT;
		}
		else
		{
			print "File $file does not exist\n";
		}
	}
	close OUT;
}