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

use strict;

# list the BUSCO fasta files in busco_seqs
my @usc_buscos=split(/\s+/,`ls busco_seqs`);

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


# cycle through each and launch a multiple sequence alignent using MAFFT
my $counter=0;
foreach my $busco (@usc_buscos) {
	my $out=$busco;
	$out=~s/.fas/.aln/;
	`mafft --quiet busco_seqs/$busco > busco_alns/$out`;
	my $trm=$out;
	$trm=~s/.aln/.aln.trm/;
	`trimal -in busco_alns/$out -out busco_alns/$trm -strictplus`;
	$counter++;
	if( ($counter % 10) == 0) { print "Aligned & trimmed $counter universal SC BUSCOs\n"; }
}

print "DONE - aligned & trimmed $counter universal SC BUSCOs\n";