Are you saying that given the line 
>hsa-let-7a-5pTGAGGTAGTAGGTTGTATAGTT

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the Perl code you've shown splits it into two lines? 
hsa-let-7a-5p
TGAGGTAGTAGGTTGTATAGTT

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Well you "can't get your head around how it's actually doing it" because it doesn't. But shouldn't fasta files have headers on separate lines? That is, aren't header and body different lines to begin with? 
>hsa-let-7a-5p
TGAGGTAGTAGGTTGTATAGTT

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In reply to Re: Not sure how it's working? by Anonymous Monk
in thread Not sure how it's working? by theward

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