use strict;

# this simply gives us some sample data, just like
# you would have gotten from doing @data = <FILE>
my @data = split $/, <<EOF;
1,comp1,type1
2,comp2,type2
3,comp3,type3
EOF
my @data2 = split $/, <<EOF;
1,comp1,type1,doc1,ref1
2,comp2,type2,doc2,ref2
3,comp3,type3,doc3,ref3
4,comp4,type4,doc4,ref4
5,comp5,type5,doc5,ref5
EOF
# end of sample-data

# figure out how many columns there are in @data
my $num_cols = () = $data[0] =~ /,/g;

# create hash-keys based on the number of columns
my %d2keys;
$d2keys{join ',', (split /,/)[0..$num_cols]} = $_ for @data2;

# delete duplicates
delete @d2keys{@data};

# and we're left with the ones that differ...
my @diff = values %d2keys;

# proof that it worked :)
print $_,$/ for @diff;