thanks a lot! i wrote this code in an attempt of reading and working with all the files in a directory but it doesnt work... yet if i specify the path of one file i get results im still a perl beginner so don´t laugh at my code ^^ thanks! 
print "Enter a directory´s path to work with all files in a folder or 
+a single file path\n\n";
chomp(my $input =<STDIN>);

if ($input =~ /./){      ### attempt of recognizing a file extention
    $datei = $input;
    open(my $fastd,'<', $datei) or die "die datei $datei wurde nicht g
+eöffnet: $!\n";

    while (my $line = <$fastd>) {  #reading fasta file
        chomp $line;
        if ($line =~ /^>/) {
            $header = $line;
            $header =~ s/>//g;
            
        }
        else {
            $sequences->{$header} .= $line
        }
    }
    
}elsif($input =~ /[^.]/){  #### attempt of recognizing just a folder b
+ut i know it wont work always
    
    $path = $input;
    
    opendir my $DIR, $path or die " the directory couldn't be opened\n
+";
    
    my @folder = grep -f "$path/$_", readdir $DIR;

    for my $file (@folder){
        open (my $fastd ,'<', "$path/$file") or die "the file $file co
+uldn't be opened: $!\n";
        
        while (my $line = <$fastd>) {  #reading fasta file
            chomp $line;
            if ($line =~ /^>/) {
                $header = $line;
                $header =~ s/>//g;
                
            }
            else {
                $sequences->{$header} .= $line
            }
        }
    }
}

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In reply to Re^2: working with directories by madM
in thread working with directories by madM

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