I want to set to paragraph mode because each of my entries is multiple lines long and is separated by a new line. So, I was reading about perl, it said I can use the paragraph mode to specify that. As I said, I'm new and still learning, let me know if it's wrong. Also, when I ran the code after correcting what you suggested, it gave me the following errors:
Use of uninitialized value $count_in in printf at ../remove_duplicate_genes.pl line 34.
0 total records read from 'enzymes.fasta'
Use of uninitialized value $count_out in printf at ../remove_duplicate_genes.pl line 35.
0 records written to 'duplicate_gene_entries_in_enzymes.fasta' after removing duplicate entries
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