#!/usr/bin/env perl
use strict;
use warnings; 
use File::Path qw/make_path/;
use Cwd;

my $dir = cwd();

opendir (my $dh, $dir) or die "Unable to open current directory! $!\n";
my @subdirs = readdir $dh or die "Unable to read directory! $!\n";
closedir $dh;

my $result_path = "$dir/results";
make_path("$result_path");

for my $subdir ( sort @subdirs ) {

chdir($dir);

next unless -d $subdir;

make_path("$result_path/$subdir");

my $search_text1 = qr/atom/;
my $infile1="$subdir/input.txt";
my $outfile1="$result_path/output";
    open my $in_fh1, '<', $infile1  or die qq{Failed to open "$infile1" for writing: $!};
    open my $out_fh1, '>', $outfile1 or die qq{Failed to open "$outfile1" for writing: $!};
  while (<$in_fh1>) {
      next unless /$search_text1/;
      my @fields1 = split;
      print $out_fh1 join("\t", @fields1[1]), "\n";
      }
  close($in_fh1);
  close($out_fh1);

chdir("..");

}