#!/usr/bin/perl
# The first line might be #!/usr/local/bin/perl etc 
# depending on the system.
#
# Do not delete this comment.#####################

if ( $#ARGV < 0 ) { 
	print "usage: $0 infile_root.\n";
	print "This script reads two files **.fa and **.p.table\n";
	print "and checks duplication. Output is a sorted list:\n";
	print "**.gfa and **.g.table.\n";
	print "This version is used when the sizes of table and list are identical.\n";
	exit 1;
}

$| = 1;

$infile_root = $ARGV[0];
$fafile = $infile_root . ".fa";
$ptable = $infile_root . ".p.table";
print "Input files are $fafile and $ptable.\n";
open(FAFILE, $fafile) || die "Unable to open file: $fafile.\n";
open(PTABLE, $ptable) || die "Unable to open file: $ptable.\n";

@tabledata = <PTABLE>;
close PTABLE;
@sorted_tabledata = sort @tabledata;
$number_tabledata = @tabledata;

@fadata = ();
$i = 0;
while(<FAFILE>) {
	$line = $_;
	if ( $line eq "\n" ) {
		next;
	}
	if ( $line =~ /^\>/ ) {
		chomp($line);
		$line =~ s/^\>//;
		$line = $i++ . "\t" . $line;
		push(@fadata,$line);
	}
}
close(FAFILE);

@sorted_fadata = sort fasort @fadata;
$number_fadata = @fadata;


sub fasort {
	@a1 = split(/\t/,$a);
	@b1 = split(/\t/,$b);
	return $a1[1] cmp $b1[1];
}

print "Number of items in $ptable = $number_tabledata.\n";
print "Number of items in $fafile = $number_fadata.\n";

$error = 0;
print "\n";
for( $i = 0; $i < $number_tabledata - 1; $i++ ) {
	print "\r";
	print $i;
	$line = $sorted_tabledata[$i];
	$line2 = $sorted_tabledata[$i+1];
	chomp($line);
	chomp($line2);
	@items = split(/\t/,$line);
	@items2 = split(/\t/,$line2);
	if($items[0] =~ /ORF\s+/) {
		print "Name should not be simply ORF in $ptable line $i.\n";
		$error += 1;
	}
	if ( $items[0] eq $items2[0] ) {
		print "Name duplication detected in $ptable line $i: $items[0].\n";
		$error += 1;
	}
}

print "\n";
for( $i = 0; $i < $number_fadata - 1; $i++ ) {
	print "\r";
	print $i;
	$line = $sorted_fadata[$i];
	$sorted_fadata[$i] = $i . "\t" . $sorted_fadata[$i];
	$line2 = $sorted_fadata[$i+1];
	chomp($line);
	chomp($line2);
	@items = split(/\s+/,$line);
	@items2 = split(/\s+/,$line2);
	if($items[1] =~ /ORF\s+/) {
		print "Name should not be simply ORF in $fafile line $i.\n";
		print "$sorted_fadata[$i]\n";
		$error += 1;
	}
	if ( $items[1] eq $items2[1] ) {
		print "Name duplication detected in $fafile sequence $i: $items[1].\n";
		$error += 1;
	}
}
$sorted_fadata[$i] = $i . "\t" . $sorted_fadata[$i];

if ( $error > 0 ) {
	print "Error in names was found. $error errors.\n";
	exit 1;
}

if ( $number_fadata != $number_tabledata ) {
	print "Number of items in $ptable is not equal to the number of sequences in $fafile.\n";
	print "They are, respectively, $number_tabledata and $number_fadata.\n";
	exit 1;
}

print "\n";
$error = 0;
for( $i = 0; $i < $number_tabledata; $i++ ) {
	print "\r";
	print $i;
	$line = $sorted_tabledata[$i];
	chomp($line);
	@items = split(/\t/,$line);
	$line2 = $sorted_fadata[$i];
	chomp($line2);
	@items2 = split(/\s+/,$line2);
	if ( $items[0] eq $items2[2] ) { last };
	for( $j = 0; $j < $number_fadata; $j++ ) {
		$line2 = $sorted_fadata[$j];
		chomp($line2);
		@items2 = split(/\s+/,$line2);
		if ( $items[0] eq $items2[2] ) { last };
	}
	if ( $j == $number_fadata ) {
			print "Name in $ptable is not found in $fafile: $items[0].\n";
			$error += 1;
	}
}

if ( $error > 0 ) {
	print "Name inconsistency error was found. $error errors.\n";
	exit 1;
}

@recovered_fadata = sort(numeric @sorted_fadata);

sub numeric { 
	@a1 = split(/\t/,$a);
	@b1 = split(/\t/,$b);
	return $a1[1]<=>$b1[1];
}


#open(TABLE, "> table") || die "Unable to open file: table.\n";
#print TABLE @recovered_fadata , "\n";
#close TABLE;

print "\n";
print "Making fa file and modifying gene name ...\n";
print "and making gclust table ...\n";

$gfafile = $infile_root . ".gfa";
$gtable = $infile_root . ".g.table";
print "Output files are $gfafile and $gtable.\n";

open(GTABLE, "> $gtable") || die "Unable to open file: $gtable.\n";
print GTABLE "GCLUST_TABLE3\t$number_tabledata\n";

if ( -f $gfafile ) {
	system ("rm -f $gfafile" );
}
open(FAFILE, $fafile) || die "Unable to open file: $fafile.\n";
open(OUT, "> out") || die "Unable to open temporary file: out.\n";
$i=1;
$k_bak = 0;

while(<FAFILE>){
	print "\r";
	print $i;
	$line = $_;
	if($line =~ /^\>/){
		$line =~ s/^\>//;
#		print OUT ">g" . $i . " " . $line;
		print OUT ">g" . $i . "\n";		# annotation is removed from the gfa file

		@z = split(/\s+/,$line);
		$gene = $z[0];
		@x = split(/\t/,$recovered_fadata[$i-1]);
		if($i - 1 != $x[1]) {
			print "Error occurred in finding items in recovered fadata.\n";
			print "i=$i, x=$x[1]\n";
			$offset = 0;
		}
		else {
#			$offset = $x[0] - 1;
			$offset = $k_bak;
			if($offset < 0){
				$offset = 0;
			}
		}
		for( $j = 0; $j < $number_tabledata; $j++ ) {
			$k = $j + $offset;
			if($k >= $number_tabledata) {
				$k -= $number_tabledata;
			}
			$line2 = $tabledata[$k];
			chomp($line2);
			@linelist = split(/\t/, $line2);	#split line with a tab
			if($linelist[0] eq $gene){
				$k_bak = $k;
				$annotlen = length($linelist[2]);
				if ( $annotlen > 255 ) { 
					$newannot = substr($linelist[2],0,254);
					$linelist[2] = $newannot;
					$tabledata[$j] = $linelist[0] . "\t" . $linelist[1] . "\t" . $linelist[2] . "\n";
				} elsif($annotlen == 0) {
					$linelist[2] = "no description";
					$tabledata[$j] = $linelist[0] . "\t" . $linelist[1] . "\t" . $linelist[2] . "\n";
				}
				$line2 = $i . "\t" . $line2 . "\n";
				print GTABLE $line2;
				last;
			}
		}
		if($j ==$number_tabledata){
			print STDERR "\nError! Item $gene is not found in the p.table.\n";
		}
		$i++;
	}
	else {
		print OUT $line;
	}
}
close GTABLE;
close OUT;
close FAFILE;

system ("mv out $gfafile");

print "Now $gtable and $gfafile are ready.\n";

#end