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

#usage example: perl /path_to_script/listret.pl -p /path_to_lists_dir -f /path_to_fasta/FastaFile.faa

my ($path,$fasta);
GetOptions(
    'path=s'          => \$path,
    'fasta=s'          => \$fasta,
    );
#print "$path\n";
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;

for my $file (@files) {
     
   if($file=~/(\w+)\.fasta/){
            
	$name = "$1";
open (INFILE2, "$path/$name.txt") || die ("cannot open input file");
	chomp(my @lista = <INFILE2>);
	$/ = "\>";
open (INFILE, "$path/$name.fasta") || die ("cannot open input file");
	chomp(my @data = <INFILE>);
open  OUT,'>'."$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";
	}
}