Modules

 glob pickle random string sys

 Functions JumpWithinKMedoids_cluster(distanceMatrix, kmax=10, num_cycles=5, max_kMedoids_iterations=1000, min_dist=0.14999999999999999, seeds=None, verbose=0, print_fnctn=None, data=None)(There are better choices)  Increases k over a range (1-kmax) and selects k for which the change from k-1 "within_distance" is largest. MinWithinKMedoids_cluster(distanceMatrix, k, num_cycles=5, max_kMedoids_iterations=1000, seeds=None, verbose=0, print_fnctn=None, data=None, return_WD=None)Like original KMedoids_cluster, but the optimal iteration is picked based on  having the minimum 'within distance', which is computed by the withinDist function. WD = SUM_clusters (SUM_motifs (SUM_inter_motif_distances)))   There is an optional flag to return WD to the parent, in case it wants to use it decide whether to repeat with a different value of k, as in "JumpWithin" averageList(lst) bestKMedoids_cluster(distanceMatrix, kmax=10, num_cycles=5, max_kMedoids_iterations=1000, min_dist=0.14999999999999999, seeds=None, verbose=0, print_fnctn=None, data=None)Descending k:  Stop Descending when distances between medoids becomes larger than min_dist bestaveKMedoids_cluster(distanceMatrix, kmax=10, num_cycles=5, max_kMedoids_iterations=1000, min_dist=0.14999999999999999, seeds=None, verbose=0, print_fnctn=None, data=None, kmin=0)[Ben's Current pick 12-02-03] Descending: Compute ave dist of members of a cluster to each of the other medoids. If any average distances are too small (