# 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`);

# hash to store species and eogs and aligned sequences
undef my %eog2spe2seq;
undef my %specs;
# array to store eog and species lists
my @eogs=();

# cycle through each and save data
foreach my $busco (@usc_buscos) {
	my $eog='';
	if($busco=~/(EOG\S{8})/) { $eog=$1; }
	open(IN,$busco) || die $!;
	my @alllines=<IN>;
	close(IN);
	my $fasta=join("\n",@alllines);
	my @eachfasta=split(/>/,$fasta);
	shift(@eachfasta);
	foreach my $fas (@eachfasta) {
		my @lines=split(/\n/,$fas);
		my $header=shift(@lines);
		my $spe='';
		if($header=~/^(\S{6})/) { $spe=$1; }
		my $seq=join("",@lines);
		$eog2spe2seq{$eog}{$spe}=$seq;
		$specs{$spe}=1;
	}
	push(@eogs,$eog);
}

# print out concatenated sequences
open(OUT,">concatenated_buscos.aln") || die $!;
foreach my $spe (sort keys %specs) {
	print OUT ">$spe\n";
	foreach my $eog (@eogs) {
		print OUT $eog2spe2seq{$eog}{$spe};	
	}
	print OUT "\n";
}
close(OUT);