# Author: Robert Waterhouse
#!/usr/local/bin/perl

use strict;

# list the BUSCO trimmed alignment files in busco_alns
my @usc_buscos=split(/\s+/,`ls busco_alns/*.trm`);

# make directory to keep all your trees
if(-d "busco_trees") { `rm -r busco_trees`; }
`mkdir busco_trees`;


# cycle through each and launch a tree estimation using RAxML
my $counter=0;
foreach my $busco (@usc_buscos) {
    my $out=$busco;
    $out=~s/.aln.trm//;
    $out=~s/busco_alns\///;
    `raxmlHPC-SSE3 -s $busco -n $out -m PROTGAMMAJTT -p 12345 -w /home/student/rmw2/busco_trees`;
    $counter++;
    if( ($counter % 10) == 0) { print "Built $counter trees\n"; }
    if($counter==30) { print "Stopping after 30 trees\n"; last; }
}

print "DONE - built $counter trees\n";