While writing this post, I just thought: why Regex? So I came up with another solution, not elegant, but it seems to work just fine.
use strict;
use warnings;
require Text::Extract::Word;
Text::Extract::Word->import( qw(get_all_text) );
my $InputFileReadable ='Input.doc';
my $content = get_all_text($InputFileReadable);
#detecting structure
my ($header, $body)= split /(\a)\1+/, $content;
my $NrSeparators = () = $header =~ /\a/g;
my @cells = split(/\a/, $content);
my $count=0;
open(FH, '>', "Output.txt") or die $!;
foreach (@cells){
$count++;
print FH $_;
if ($count eq $NrSeparators+2){
print FH "\n";
}else{
print FH "\t";
}
$count = 0 if $count eq $NrSeparators+2;
}
close(FH);
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