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while (<>) {  # or maybe using a file handle, like <IN>
   # do stuff...
}

while (<>) {
    next if ( /^\s*;/ );  # skip if first non-space char is ";"
    # now do stuff...
}

while (<>) {
    next if ( /^\s*;/ or /;;/ );
    # now do stuff...
}

    ^    -- line begins with...
    \s*  -- zero or more white-space characters
    ;    -- followed by a semi-colon
or
    ;;   -- there are two semi-colons together anywhere in the line