I tried to follow your code to figure out what was going on, but my head started hurting, so instead I'll offer a simpler way to do what I think you're trying to do (which I'm not really clear on, so I could be way off base). Assuming that you're trying to massage lines in this format:

YAL038W 1.1 2.4 4.1 YCL040W 1.1 1.6 1.8 9.11 0.0402128119838095
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Into a structure like so:

%hash = ('YAL038W' => [1.1, 2.4, 4.1],
         'YCL040W' => [1.1, 1.6, 1.8, 9.11, 0.0402128119838095],
         ...);
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then I would do something like so with each line:

my $cur_identifier = '';
chomp $line;
foreach my $element (split /\s+/, $line) {
  if ($element !~ /\d+(?:\.\d+)?/) { # matches int or float numbers
    $cur_identifier = $element;
  }
  else {
    push @{$hash{$cur_identifier}}, $element;
  }
}
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This splits the line on whitespace, then loops through the resulting list. Whenever it encounters an element that doesn't look like a number, it considers it the start of a new 'identifier' (hash key), and subsequent numbers are pushed onto the array referenced by that key, until the next identifier is reached.