#!/usr/bin/perl
# The first line might be #!/usr/local/bin/perl etc 
# depending on the system.
# gbk2ptable.pl: 
# Do not delete this comment.#####################

if ( $#ARGV != 2) { 
        print "usage: $0 infile gbkDBname newDBname.\n";
        print " infile is a gbk file.\n";
        print " gbk file is converted to a FASTA file and a p.table file.\n";
        exit 1;
}

$| = 1;

$infile = $ARGV[0];
$gbkDBname = $ARGV[1];
$newDBname = $ARGV[2];
@infile_list = split(/\./ , $infile);
$cdsfile = $infile_list[0] . ".cds";
$command = "extcds " . $infile . " " . $cdsfile;
system $command;

#$fafile = $infile_list[0] . ".fa";
$fafile = $newDBname . ".fa";

open(INFILE, $cdsfile) || die "Unable to open file: $cdsfile.\n";
open(OUT, "> $fafile") || die "Unable to open file: $ptable.\n";
$counter = 1;
while(<INFILE>){
# This part should be edited for each use.
	if ( $_ =~ /^\>/ ){
        $_ =~ s/^\>$gbkDBname/\>$newDBname/;
#       unless ( $_ =~ /^\>Pm3_Pro/ ) {
#           @items = split(/\s+/, $_);
#           @name = split(/_/, $items[0]);
#           $newname = "g" . $counter;
#           $_ =~ s/$name[1]/$newname/;
#           chop($_);
#           $_ = $_ . $name[1] . "\n";
#       }
		$counter++;
	}
	print OUT $_;
}
close(INFILE);
close(OUT);

$tempfile = $infile_list[0] . ".temp";
$command = "genlist " . $fafile . " " . $tempfile;
system $command;

#$ptable = $infile_list[0] . ".p.table";
$ptable = $newDBname . ".p.table";

open(INFILE, $tempfile) || die "Unable to open file: $tempfile.\n";

open(OUT, "> $ptable") || die "Unable to open file: $ptable.\n";

$line = <INFILE>;
$line = <INFILE>;
$line = <INFILE>;

while(<INFILE>){

	if( $_ eq ".\n") {
		next;
	}

	$_ =~ s/^ID=//;
	$_ =~ s/\,\ /\t/;
	$_ =~ s/\ residues\,\s+/\t/;
	$_ =~ s/\d+\ complement/1/;
	$_ =~ s/\d+\ \d+\s+\d+\ //;
	$_ =~ s/\;.*\;//;

	print OUT $_;
}

close(OUT);
close(INFILE);

$command = "rm -f " . $cdsfile;
system $command;
$command = "rm -f " . $tempfile;
system $command;
# end