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cog_class(\@c1_uniq_cog_ids, $name1);

    my $c1_uniq_cog_ids = shift;
    my $name = shift;

#!/usr/bin/perl -w
use strict;
...
        # BLAH BLAH
    }
}

foreach my $id (@{c1_uniq_cog_ids}) {
    # Do stuff
}

for (@{c1_uniq_cog_ids}) {
    # Do stuff
}