You don't check for errors so it's likely that opening the file failed and you didn't notice.
Either use the autodie pragma at the top of your file:
use autodie;
... or manually check for failure:
open PROTEINFILE, $proteinfilename or die "Couldn't open '$proteinfilename': $!";
In reply to Re: Cannot open file in Strawberry Perl
by Corion
in thread Cannot open file in Strawberry Perl
by Anonymous Monk
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