#! perl -slw
use strict;



if (scalar(@ARGV) != 1) {
    print "\n";
    print "Usage: script.pl <alignment file>";
    print "\n";
    exit();
  }

my ($FILENAME) = @ARGV; #read in file
open(DATA, $FILENAME);

my( $id, %accu, @order );

## remove existing files    
my $remove = "new_alignment_".$FILENAME;  #remove any existing results file
    if (unlink($remove) == 1) {
                        print "Existing \"$remove\" file was removed\n";
                          }



## generate a temporary storage file    
my $outputfile = "new_alignment_".$FILENAME; #make a big file in which the final results will be printed
    unless ( open(POS, ">>$outputfile") ) {
	print "Cannot open file \"$outputfile\" to write to!!\n\n";
	    exit;
	    }

while( <DATA> ) {
    chomp;
    if( m[^(\S+_\S+_\S+)\s+(.+)\s*$] ) {
        $id = $1;
        unless( exists $accu{ $id } ) {
            push @order, $id;
            $accu{ $id } = $2;
        }
        else {
            $accu{ $id } .= ' ' . $2;
        }
    }
    else {
        $accu{ $id } .= ' ' . $_;
    }
}

for my $key ( @order ) {
    printf POS "%-10s %s\n", $key, substr( $accu{ $key }, 0, 55, '' );
    print POS substr( $accu{ $key }, 0, 66, '' ) while length $accu{ $key };
    print POS '';
}