Separate the calculate_threshold function out

[dpear]

Now, there is a function that returns the read count threshold, along with other necessary column calculations, which can be used to get the specific number that refers to the read count threshold. Hopefully this will make downstream automation with Qiita easier.

This new function can be found under _methods.py as calculate_threshold which has 5 outputs the first of which min_freq is the read count threshold.