I'm very new to Perl and am struggling to figure out how to loop through ~15,000 records and analyse different sized matrices within each record. Having tried a lots of different ways (while loops, unless, next if ... etc), to accommodate the variance in size ... I need help!

use strict;
use warnings;

open(MOTIFS, "all_motifs.txt") or die("Unable to open file");

# Read the first 7 lines of metadata.
# # Assuming there are always 7 lines of metadata.
foreach (1..121)
  {
  foreach (1..7)
     {
     # Read a line of data.
     my $header_data = <MOTIFS>;

     # Remove the end of line character.
     chomp $header_data;

     # Split the string into 2 parts, using white space as a separator
+.
     my ($lable, $string) = split /\s+/, $header_data, 2;

     # only pay attention to the "Motif" line.
     next if ($lable ne 'Motif');
     print "$string ";
     }
[download]

The problem's with this next bit:

  # Process the next lines of data until line containing string "TF   
+   Unknown" is reached.
foreach (<MOTIFS>)
  {
        # Remove the end of line character.
        chomp my $line;
        # Process lines until "TF Unknowm'
        while ($line ne 'TF      Unknown')
          {
          # Declare a variable to hold the data in the file.
          my %base_pairs;

          # Split the string into 5 parts, using whitespace as a separ
+ator.
          # Assuming the Position is always in the same order in the f
+ile.
          (undef, $base_pairs{A}, $base_pairs{C}, $base_pairs{G}, $bas
+e_pairs{T}) = split /\s+/, $line, 5;
          my @letters = keys %base_pairs;

          # Start with the first column value and make it the max. val
+ue.
          my $max = pop @letters;

          # Compare each value to the maximum.
          foreach my $letter (@letters)
             {
             # What if two (or more) values are equal???
             if ($base_pairs{$max} < $base_pairs{$letter})
                 {
                 # The current value was greater than the maximum, so 
+make it the new maximum.
                 $max = $letter;
                 }
             }

  # Print the letter representing the maximum value.
          print $max;
         }
      }
   }
# print an end of line character.
print "\n";
[download]

This is what a few records look like:

TF      Unknown
TF Name Unknown
Gene    ENSG00000113916
Motif   ENSG00000113916___1|1x3
Family  C2H2 ZF
Species Homo_sapiens
Pos     A       C       G       T
1       0.664794        0.13099 0.0810125       0.123203
2       0.675621        0.0396475       0.144967        0.139764
3       0.0913393       0.0396819       0.847004        0.0219745
4       0.850414        0.0522149       0.0519174       0.0454536
5       0.89157 0.00962148      0.0845269       0.0142814
6       0.122389        0.0875591       0.0734604       0.716591
7       0.226696        0.00745549      0.745549        0.0202999
8       0.156228        0.151994        0.128767        0.563011
9       0.22083 0.561173        0.12007 0.0979266
10      0.507656        0.0711684       0.0652815       0.355894
TF      Unknown
TF Name Unknown
Gene    ENSG00000113916
Motif   ENSG00000113916___1|2x3
Family  C2H2 ZF
Species Homo_sapiens
Pos     A       C       G       T
1       0.538498        0.157305        0.157633        0.146564
2       0.0728444       0.00877167      0.877166        0.0412175
3       0.959269        0.0131077       0.0159611       0.0116621
4       0.852439        0.0238831       0.0168134       0.106864
5       0.57332 0.0688014       0.181385        0.176494
6       0.139513        0.0747988       0.737607        0.0480813
7       0.735484        0.0912993       0.09091 0.0823067
TF      Unknown
TF Name Unknown
Gene    ENSG00000113916
Motif   ENSG00000113916___1|3x3
Family  C2H2 ZF
Species Homo_sapiens
Pos     A       C       G       T
1       0.616484        0.0886488       0.24602 0.0488468
2       0.0971289       0.591289        0.134781        0.176801
3       0.0715039       0.0237142       0.0432674       0.861514
4       0.73769 0.117011        0.059703        0.0855963
5       0.0728444       0.00877167      0.877166        0.0412175
6       0.959269        0.0131077       0.0159611       0.0116621
7       0.852439        0.0238831       0.0168134       0.106864
8       0.57332 0.0688014       0.181385        0.176494
TF      Unknown
TF Name Unknown
Gene    ENSG00000113916
[download]

Thank you!