#!usr/bin/perl
# Programmer: Rachel Bingham
# Date: 29 April 2009
# Usage: 'perl swap --f=[filename]
# Documentation: Swaps input and output files of training data records
#                to have reversed input/output neural nets. Creates an 
#                output file renamed by replacing 'single' with 'reverse'.
#                Tested on file:
#                  /training_data/dunbrack-30pc-1763-1.single-str2
# Notes: Script not optimized. It's a quick one to just do the job.
use strict;
use warnings;
use Getopt::Long;
my ($infile, $outfile) = undef;
my ($to_replace, $replace_with) = ("single", "reverse");
my $options = GetOptions("f=s"=>\$infile);
open(IN_FILE, $infile) or die("Cannot open file: $infile\n");
$outfile=$infile;
$outfile =~ s/$to_replace/$replace_with/g;
open(OUT_FILE, "+>$outfile") or die("Cannot open file for writing: $outfile\n");
# Temporary array to hold the input and output file strings
my @swap_array = ("","","");
# Run through the file line by line parsing by whitespace
while(my $line = <IN_FILE>) {
    if($line =~ m/(^($|InfilePrefix[\s+]$))/i) {print(OUT_FILE $line); next;}
    chomp($line);
    @swap_array = split(/ /, $line);
    print(OUT_FILE $swap_array[0]," ",$swap_array[2]," ",$swap_array[1],"\n");
}
close(OUT_FILE) or die("Cannot close file: $outfile\n");
close(IN_FILE) or die("Cannot close file: $infile\n");