Hi guys!
Many thanks for all the posts!
My problem is actually down to why this:

print ">$protein\n$respective_seq\n";
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works, and I see the results on my screen (so the if block is executed normally, while this:

print OUT ">$protein\n$respective_seq\n";
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does not work! The file IS created, but nothing is printed inside...I tried also with open OUT, '>', "outfile"; but no luck!
I don't get a warning either...
I am so confused, I can't make sense of it...