It looks like your data has a space at the start of each line. If so, try

while(<$HANDLE>) {
    chomp;
    s/^\s+//; # remove leading spaces
    my ($freq, $data) = split /\s+/, $_, 2;
    $inputdata->{$freq}->[$filenumber] = $data;
}

[download]
poj

In reply to Re^3: Merging Columns from multiple files into a single file by poj
in thread Merging Columns from multiple files into a single file by ikhan

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