Untested, beware of typos: 
$ref = [map {$$_[0]}
        sort {$$a[1] cmp $$b[1]}
        map {my $srn = $_->seq_region_name;
             [$_, sprintf "%03d;%s", ($srn =~ /[0-9]/ ? ($srn, "") : (
+0, $srn))]}
        @$ref];

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In reply to Re: sorting by numbers then alphabetically by JavaFan
in thread sorting by numbers then alphabetically by Anonymous Monk

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