#!usr/bin/perl -w
use strict;
use Getopt::Long;

#usage example: perl /path_to_script/bay_seqret.pl -p /path_to_lists -f /path_to_fasta/FASTA_file.faa

my ($path, $fasta);
GetOptions(
    'path=s'          => \$path,
    'fasta=s'          => \$fasta,
    );
chdir $path or die "ERROR: Unable to enter $path: $!\n";
opendir (TEMP , ".");
my @files = readdir (TEMP);
closedir TEMP;
my $name;
my $found=0;
my $totalist=0;
$/ = "\>";###CHANGED HERE TO SPLIT FASTA by ">"
open (INFILE, "$path/$fasta") || die ("cannot open input file");
chomp(my @data = <INFILE>);
print"@data\n";
$/ = "\n";####"REGENERATED" HERE NOT TO INTERFERE WITH THE REST OF THE DATA PROCESSING
for my $file (@files) {
	if($file=~/(\w+)\.txt/){
		$name = "$1";
		print"Lista: $path/$name.txt\n";
		open (INFILE2, "$path/$name.txt") || die ("cannot open input file");
		chomp(my @lista = <INFILE2>);
		open  OUT,'>'."$path/$name.out" or die "ERROR: Unable to open $file $!\n";
		foreach my $li (@lista){
			chomp $li;
			print"$li\n";
			$totalist++;
			for(@data){
				if(/$li/){
				    $found++;	    
				    print ">"."$_\n"; 
				    print OUT ">"."$_\n";
				}
			}
		}
		print "For $name we found $found of a total $totalist\n";
	}
}