my @file = "$_";
[download]

Pass all the lines to the sub, and assign it as (note the better name):

my @lines = @_;

# ...

sorting(<>);
[download]

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
[download]

Hi! Thanks for the comment! I have corrected that. Here is the upated script:

 
sonya$ vi sorting.pl
#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;

my $version="0.2";
my $files_match="";
my $files_dir="";
my $file_name="";
my $help_flag="";
my $version_flag="";

GetOptions(
           'm|match=s' => \$files_match,
           'd|directory=s' => \$files_dir,
           'h|help' => \$help_flag, 'v|version' => \$version_flag,
);

sub sorting {
my @lines = @_;
my @sorted = map { $_->[0] }
             sort { $a->[1] <=> $b->[1] }
             map { my ($x) = $_ =~ /VerNumber:\((\d+)/i; [$_, $x]; }
             @lines;
print FILE for @sorted;
}

if (($files_match ne "") and ($files_dir ne "")) {
        chdir("$files_dir") or die "$!";
        opendir (DIR, ".") or die "$!";
        my @files = grep {/$files_match/} readdir DIR;
        my $files_size = $#files + 1;
        my $index_file = 1;
        print "Files to process: $files_size\n";
        close DIR;

        foreach (@files) {
                open(FILE, ">./sorted/$_.sort") or die $!;
                my @singlefile = $_;
                print "Processing $index_file of $files_size files: $_
++\n";
                local @ARGV = @singlefile;
                while(<>){
                       sorting($_);
                }
                close(FILE);
                $index_file++;
                print "OK: Sorted @singlefile \n";
        }
    } elsif ((!$help_flag) and (!$version_flag)){printHelp();}
"sorting.pl" [New] 49L, 1391C written
[download]

However, I am still getting the unchanged files as a result:

sonya$ ./full.pl -d /home/sonya/test/ -m file
Files to process: 3
Processing 1 of 3 files: file1.txt+
OK: Sorted file1.txt
Processing 2 of 3 files: file2.txt+
OK: Sorted file2.txt
Processing 3 of 3 files: file3.txt+
OK: Sorted file3.txt
sonya$ diff /home/sonya/test/file1.txt /home/sonya/test/sorted/file1.t
+xt.sort 
sonya$
sonya$
[download]

The standalone sorting script is working so there is something wrong with my code.

In your program main loop, you still iterate over each file and call sorting. If you want to sort the content of all files, either concatenate all files before starting your program or change your program to first read the content of all files and then sort it, instead of reading and writing a single file. This will mean moving some of the code out of sorting, especially the part where it reads in the whole file, and the part where it writes the sorted file.

Thank you for your quick replay. I cannot use the option to concatenate files as I want to sort the content of all files, one by one, and place the new files (with the same name) to the new folder. This is important because of other steps in my procedure. Therefore I need to first read the content of all files an then sort them. When you say moving some of the code out of sorting, which part excatly are you refering to? I am sorry for the additional question, but I am a newbe in Perl and I still find it hard to understand the syntax. Thanks!

One way to do this is open both the input and output file handles and pass them both to the sorting routing. Your code used a bare word name, FILE for the output file. It is not so obvious that FILE is actually changing as the program runs. Better to use a lexical file handle and pass it to sorting(). FILE is global in scope and you were using that to pass a variable to sorting(), which is not a good idea.

I prefer to close() the filehandles at the same level of code as the open().

I do have some issues with the variable names. These names are important. For the "counter", perhaps $file_num, $file_counter, $filecnt or some such. "$index_file" is confusing. First of all this is not any kind of an "index". Anyway, I suggest you spend a bit more time considering names.

Unless the for (or foreach) loop is really short and obvious, I prefer to declare an actual name for the loop variable rather than using $_; When you into the body of the loop, $_ is so generic that it can be confusing about what that really is. An extra "my variable" is a "cheap" thing to create and usually well work the effort.

Update: I went ahead and added a few lines to make this a complete program that I could test. Glob is a bit easier than readdir for a very simple case like this. You also had a number of lines of code where I couldn't figure out what the intent was, so I deleted them.

#!/usr/bin/perl
use strict;
use warnings;

if (!-d "sorted")
{
    mkdir "sorted" or die "unable to create dir sorted $!";
}

my @files2sort = <file*.txt>;  #just use glob to get names
my $curfilenum =1;

foreach my $file (@files2sort)
{
   open my $fh_in, '<', $file  or die "$file failed to open $!";
   open(my $fh_out, '>', "./sorted/$file.sort") or die "cannot create 
+out $file.sort $!";
   
   print "Processing ".$curfilenum++." of ".@files2sort." $file\n";
   sortfile($fh_in, $fh_out);

   close ($fh_out);
   close ($fh_in);
   print "OK: Sorted $file \n";
}

sub sortfile 
{
   my ($fh_in, $fh_out) = @_;
   
   my @lines = <$fh_in>;
   
   my @sorted = map { $_->[0] }
                sort { $a->[1] <=> $b->[1] }
                map { my ($x) = $_ =~ /VerNumber:\((\d+)/i; [$_, $x]; 
+}
                @lines;
      
   print $fh_out @sorted;
}    


__END__
Processing 1 of 2 file1.txt
OK: Sorted file1.txt 
Processing 2 of 2 file2.txt
OK: Sorted file2.txt 

#these names are confusing...
my $files_size = $#files + 1;
my $index_file = 1;

#better names?:
my $num_files = @files; 
# the value of an array in a scalar context is the
# number of items in the array, no need for $#files+1
# or you can just use @files in a scalar context without
# creatng $num_files at all. 

my $file_counter =1;
#  "$index_file" would mean something different
[download]

I showed some working Schwartzian Transform (ST) code at Re: Use Schwartzian transform across multiple files. As a beginner, I would certainly consider the idea of a more straightforward approach. I recommend that you master the basics before trying to use advanced techniques. I show "another way" for you below.

The sort routine selects pairs of things to "judge". The user supplied function's job is to decide: less than, equal, or greater than. In the code below, there is a lot of "extra work" because a regex has to be run twice every time a new pair of "things" is selected for comparison. The ST is faster because it calculates all of the regex's only once and saves that result in an intermediate array before the actual sort is run.

However you should consider that often this extra efficiency doesn't matter at all in the overall scheme of things. In fact, for small numbers of lines, the ST can actually be slower due to the overhead of creating the intermediate array and transforming it back to the original representation.

How fast is "fast enough" depends upon the application. If you are sorting an array of say 80,000 elements, there probably will be a user noticeable difference between algorithms. With 100-200 lines, probably not.

Once you get your code working, I encourage you to benchmark the code below vs my ST version. Make the comparison as "fair as possible". Also be aware that the second time you run the program, it will run faster because the files will be in memory disk cache and that speeds things up a lot. But even so, you probably will learn something from doing a simple benchmark exercise. I don't know what OS you are using, but also be aware that on some OS'es. Windows in particular, console I/O is an extremely "expensive" operation and takes a lot of execution time. I/O to report benchmark progress can consume so much time that it skews the results.

#!/usr/bin/perl
use strict;
use warnings;

if (!-d "sorted")
{
    mkdir "sorted" or die "unable to create dir sorted $!";
}

my @files2sort = <file*.txt>;  #just use glob to get names
my $curfilenum =1;

foreach my $file (@files2sort)
{
   open my $fh_in, '<', $file  or die "$file failed to open $!";
   open(my $fh_out, '>', "./sorted/$file.sort") or die "cannot create 
+out $file.sort $!";
   
   print "Processing ".$curfilenum++." of ".@files2sort." $file\n";
   sortfile2($fh_in, $fh_out);

   close ($fh_out);
   close ($fh_in);
   print "OK: Sorted $file \n";
}


sub sortfile2
{
   my ($fh_in, $fh_out) = @_;
      
   my @lines = <$fh_in>;
      
   @lines = sort by_version @lines;
         
   print $fh_out @lines;  #can do a sort "in place"
                          #separate @sorted var is not needed.

}

sub by_version
{
   my ($verA) = $a =~ /VerNumber:\((\d+)/i;
   my ($verB) = $b =~ /VerNumber:\((\d+)/i;
          $verA <=> $verB    #returns -1,0,+1
}

__END__
Processing 1 of 2 file1.txt
OK: Sorted file1.txt 
Processing 2 of 2 file2.txt
OK: Sorted file2.txt
[download]

Hi Marshall!

Thank you so much for your detailed response and guidance. I am a newbe in Perl and I got a bit lost with my attempt using as you say advanced options, so I really appreciate your comments. I agree that using the "glob" is easier and much more clear to me in this specific case.

I decided to go with the ST code since I have 16000 files with approx. 4000 arrays each. So based on your guidance this would be the faster way.

Most importantly, the ST script you have suggested works perfectly! I have just tried it on all the files and it was done in less than 5 minutes. Later on I will test and compare both scripts. With ST script you have suggested I got the desired result and I cannot thank you enough.

It is always nice to see someone ready to share his knowledge with the world and it is a motivation for the rest of us to do the same!

Cheers!