Mercurial > repos > chemteam > fastpca
view get_clusters.py @ 3:9ca30ad95444 draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
author | chemteam |
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date | Fri, 13 Nov 2020 19:37:55 +0000 |
parents | d9f8cc3258f9 |
children |
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import argparse import collections import json import numpy as np from scipy.cluster.hierarchy import fcluster def separate_clusters(Z_fpath, threshold, min_members, output): Z = np.loadtxt(Z_fpath) branch_assignments = fcluster(Z, threshold, criterion='distance') cluster_dict = collections.defaultdict(list) for n, val in enumerate(branch_assignments): cluster_dict[branch_assignments[n]].append(n) cluster_dict = {int(k): v for k, v in cluster_dict.items() if len(v) >= min_members} with open(output, 'w') as f: json.dump(cluster_dict, f, indent=4, sort_keys=True) def main(): parser = argparse.ArgumentParser() parser.add_argument('--Z', required=True, help='File for cluster linkage array.') parser.add_argument('--threshold', type=float, required=True, help='Distance cutoff.') parser.add_argument('--min-members', type=int, required=True, help='Minimum number of members of the cluster.') parser.add_argument('--output', required=True, help='Output file.') args = parser.parse_args() separate_clusters(args.Z, args.threshold, args.min_members, args.output) if __name__ == "__main__": main()