open  OUT,'>'."$path/$name.faa" || die ("cannot open out $file $!\n");
[download]

Unless joluito has been busy making uncited changes behind the scenes (update: /msg from pryrt says changes were made), the quoted statement is not present in the OPed code. However, I agree with your point about evaluation order in this statement.

... the real problem [is] setting the global variable $/

$/ = "\>";

and then never restoring it back to "\n".

Although trollishly delivered, I agree that failure to restore $/ is a problem, likely the root problem. No one else has made this point (update: yet — but see this).

Pretty sure was stealth edited because that was the reason I called it out as incorrect and needing parens as written at the time.

The cake is a lie.
The cake is a lie.
The cake is a lie.

And Guido retired because he couldn't stand anymore the hate in that "community".

FWIW: I voted "edit", because you were clever enough to envelop valid points with trolling, I'd call this trojan trolling.

IMHO we should just reap the original (for the archive) and repost the valid points.

(Keep the horse, burn the Greeks)

Didn't expect to find such trolls in a place like this...

But anyway, he nailed it about changing the filed separator.

Here's is the FUNCTIONAL code (may indentation not be that good, and the code not obfuscated enough as to win a contest...but we need it to be mantained by different people, some of who are new to programming).

#!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 f
+ile");
        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";
    }
}
[download]

It will be gone in a minute or two because it’s not tolerated here.