First off, I have pretty much no idea what you were trying to say, your description is incomprehensible. However, just looking at your code:

my ($id_snp, $id_assay, $session,  $load_set) = @_; #these variables
my (@lines) = @_;                                   #this array
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The value of @_ doesn't change between these two lines. That means that the first four values of @lines are going to be the same as the four variables you grab on the first line. Is that what you are trying to do, or is the value of @lines supposed to be the arguments after those four?