#!/usr/bin/perl -w 
use strict;

my %opt=@ARGV;

my $opt_l=$opt{'-l'}; ## list of gene IDs 

open (LIST, "$opt_l") || die "cannot open list of gene IDs";

my @list = <LIST>;

foreach my $thing (@list) {
chomp $thing;

#write R script to convert newick trees to nexus trees

open (OUT, ">ape_nexus_convert.R");
my $script = "#!/usr/bin/env Rscript\nlibrary(\"ape\")\nmytree <- read.tree(\"RAxML_bootstrap.$thing\")\nwrite.nexus(myt
ree, file = \"$thing.R.nexus\")\nq()";
print OUT $script;
close OUT;

#execute R script

`chmod 755 ape_nexus_convert.R`;
`./ape_nexus_convert.R`;
`rm ape_nexus_convert.R`;

open(I,"$thing.R.nexus")|| die "cannot open nexus file\n";
open(O, ">$thing.nexus") || die "cannot open outfile\n";


my $check = 0;
my $count = 0;

#tweak file format

while (<I>) {

if ($_ =~ /TREE \* UNTITLED = \[&U\]/) {$count ++;}

$_ =~ s/TREE \* UNTITLED = \[&U\]/tree rep\.$count =/;

if ($_ =~ /BEGIN TAXA/){$check =1;}
	
if ($_ =~ /BEGIN TREES/) {$check = 0;} 

if (!$check) {print O $_};

}
`rm $thing.R.nexus`;
}