G'day MB123,

Welcome to the monastery.

I am unable to reproduce the stated problem. Furthermore, after removing the debug print statements (e.g. say qq(DEBUG: Line = "$line");), the output I get is: 

Coordinate   No of Strains   AA Change
703          1               AA Ala->Thr
937          1               AA Val->Leu
1804         3               AA Ser->Thr

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This appears to be exactly what you were hoping for!

Please check that the code and data you've posted is the same as that which generates the warnings you described.

-- Ken

In reply to Re: Parsing problem by kcott
in thread Parsing problem by MB123

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