The uclust calls should probably be performed with the uclust application controller in [brokit](https://github.com/biocore/brokit). @cleme do you agree? [`get_clusters_from_fasta_filepath`](https://github.com/biocore/brokit/blob/master/brokit/uclust.py#L482) might work well here (see qiime/pick_otus.py for an example of how this is being used).