$output[0] is the first element of the array @output. What you need there is the first character of $line, which is
substr($line, 0, 1) eq 'A'

[download]

Also, there is a precedence problem on your open line. Use or instead of ||, otherwise your statement means

open DATA, ( "<piRNA_Dataset" || die "..." )

[download]
which will never die.

In reply to Re: extract ouput that counts strings starting with A in the dataset by choroba
in thread extract ouput that counts strings starting with A in the dataset by MVRS

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