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1<species xxx = "sp">
...
etc.........................................

(xxxxxxs substitute real words)

sub deal_with_xml_line_by_line($){
...
 }
    }
}

1 <species xxx = "sp">
1 <sequence xx = "" xxxxx = "xxxxxxx">
...
2   <gene xx = "xxxxxxxxxxx" xxxxxx = "x">
2    <gene_seq xxxxxxx = ""  xxxxxx =  ""   xxxxxxx = "2"  xxxxxxxxx =
+ ""  xxxxx = "5999"  xxxx = "6318"  xxxxxxx = ""  xxxxxxx = ""  xxxxx
+x = "F">