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annotate get_clusters.py @ 3:9ca30ad95444 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
author chemteam
date Fri, 13 Nov 2020 19:37:55 +0000
parents d9f8cc3258f9
children
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d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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1 import argparse
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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2 import collections
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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3 import json
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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5 import numpy as np
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d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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7 from scipy.cluster.hierarchy import fcluster
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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10 def separate_clusters(Z_fpath, threshold, min_members, output):
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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11 Z = np.loadtxt(Z_fpath)
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12 branch_assignments = fcluster(Z, threshold, criterion='distance')
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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13 cluster_dict = collections.defaultdict(list)
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14 for n, val in enumerate(branch_assignments):
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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15 cluster_dict[branch_assignments[n]].append(n)
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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16 cluster_dict = {int(k): v for k, v in cluster_dict.items()
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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17 if len(v) >= min_members}
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18 with open(output, 'w') as f:
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19 json.dump(cluster_dict, f, indent=4, sort_keys=True)
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22 def main():
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23 parser = argparse.ArgumentParser()
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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24 parser.add_argument('--Z', required=True,
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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25 help='File for cluster linkage array.')
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26 parser.add_argument('--threshold', type=float, required=True,
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27 help='Distance cutoff.')
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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28 parser.add_argument('--min-members', type=int, required=True,
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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29 help='Minimum number of members of the cluster.')
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30 parser.add_argument('--output', required=True,
d9f8cc3258f9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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31 help='Output file.')
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32 args = parser.parse_args()
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34 separate_clusters(args.Z, args.threshold,
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35 args.min_members, args.output)
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38 if __name__ == "__main__":
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39 main()