# converts Nexus tree output file produced by BioPerl (with ids on trees) into TreeView-readable nexus file

use strict;

open (INTREE, "$ARGV[0]") || die $!;
open (OUTTREE, ">$ARGV[1]") || die $!;

while (<INTREE>) {
    print OUTTREE $_;
    last if /Translate/
    }


my %no;
while (<INTREE>) {
    print OUTTREE $_;
    last if /;/;
    my ($no, $id) = /(\d+)\s+('\S+')/;
    $no{$id} = $no;
    print "_$no\_\t_$id\_\n";
}

while (<INTREE>) {
    last if /End/;
    s/\(//;                 # remove one pair of parentheses
    s/('\S+?')/$no{$1}/g;
    s/\[\d+?\]//g;
    s/\);/;/;                 # remove one pair of parentheses
    print OUTTREE $_
    }

print OUTTREE "End;\n";