My apologies. I realize there's a lot of context missing here. It was my intention to simplify the code for readability, rather than to encumber everyone with other aspects of the code that are not relevant. The script is designed to read entries from an input file that are sorted by decreasing abundance, take the top-most (most abundant) entry and group everything else in the file that is similar (but less abundant). It should then move onto the next most-abundant entry that hasn't been grouped and search the remaining ungrouped entries for similarity and group them together. This repeats until the array of entries is exhausted.

I want to KEEP entries that don't meet the criteria and I want to REMOVE the ones that do, and then repeat until there's nothing left.

When I call on compare_sub it returns a value, if the value is less than or equal to a user defined value, then the entry gets printed to output and spliced out of the array. (I removed the print function from the code).

I'm still quite new at this! Thanks for the help and I hope that clarified things a bit.