#/bin/perl/

use strict;
use warnings;

my $results = "~/results"; 
my $unpacked = "~/results/unpacked"; 
my $submit = "~/submit";

 my @files;

 @files = `ls *$txt`;
 
 my $filename;

 my $seq;
 my $nr;
 my $mol;
 my $dir;
 my $step;
 my $type;

 open (my $finished, '>>', "finished.txt");
 printf $finished ("%-5s%12s%14s","Molecule","Structure","Step");
 printf $finished "\n";
 close $finished;

 foreach (@files) {
  
 /(prefix)(_)(\d+)(_)(\d+)(_)(\w+)(_)(\w+)(_)(\w+)(\.)(\w+)/;
 $filename = "$1$2$3$4$5$6$7$8$9$10$11$12$13";
 print "name of file: $filename \n";
 print "\n";
 
 $seq= $3;
 $nr = $5;
 $mol = $7;
 $dir = $9;
 $step = $11;
 $type = $13;
 
    open (my $finished, '>>', "finished.txt");
    printf $finished ("%-5s%15s%15s",$mol,$dir,$step);
    printf $finished "\n";
    close $finished;

     my $check = 0;
       
     $check = `ls | grep -c $mol\_$dir\_step\.$out`;
     print "$mol\_$dir\_$step\.$out: $check \n";
              
        if ($check == 0) {
        open my $error, '>>', 'error.txt';
        print $error "WARNING $mol\_$dir\_$step\.$out is missing \n";
        close $error; 
        }

          else {
          open my $found, '>>', 'found.txt';
          printf $found "$mol\_$dir\_$step\.$out is found \n";
          close $found;
          }
   
     $check = 0;
     
     print `rsync -ravn \*$mol\_$dir\_$step\.$out ~/results/unpacked/$mol/$dir`;

###this is where my problems start
my @step = (
   step( 'S', 6, 1, 5 ),
);

 for $step (@step) {
        print `touch $step`;
 }

  sub step {
    my ( $name, $total_length, $from, $to ) = @_;#

    my $length = $total_length - length($name);
    my $format = "${name}%0${length}d";

    return map sprintf( $format, $_ ), $from .. $to;
  }
  

    if (`ls -c *$step*`) {
    print "$step is found \n"
    }
     else {
      print "$mdstep not found \n"
     }

}