perl -d name_of_your_script.pl

##</code><code>##

# my $file = "P1GroupCExercise2_trypsin.txt";  # commented out
...
# open(FILE,$file) or die "error: unable to open file $file\n";   # commented out
while (<DATA>)     # not "<FILE>"
{
   ...
}
...

__DATA__
>Protein:HEMINF_F3_Complement_N182_S1226717_L118
|Peptide:13|Missed:0|Type:I|Enzyme:trypsin|Seq:R|
...