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annotate nxn_clustering.py @ 33:73b8c87779ae draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author bgruening
date Sat, 20 May 2017 08:31:15 -0400
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33
73b8c87779ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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1 #!/usr/bin/env python
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2 """
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3 Modified version of code examples from the chemfp project.
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4 http://code.google.com/p/chem-fingerprints/
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5 Thanks to Andrew Dalke of Andrew Dalke Scientific!
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6 """
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7 import matplotlib
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8 matplotlib.use('Agg')
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9 import argparse
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10 import os
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11 import chemfp
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12 import scipy.cluster.hierarchy as hcluster
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13 import pylab
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14 import numpy
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16 def distance_matrix(arena, tanimoto_threshold = 0.0):
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17 n = len(arena)
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18 # Start off a similarity matrix with 1.0s along the diagonal
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19 try:
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20 similarities = numpy.identity(n, "d")
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21 except:
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22 raise Exception('Input dataset is to large!')
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23 chemfp.set_num_threads( args.processors )
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25 ## Compute the full similarity matrix.
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26 # The implementation computes the upper-triangle then copies
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27 # the upper-triangle into lower-triangle. It does not include
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28 # terms for the diagonal.
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29 results = chemfp.search.threshold_tanimoto_search_symmetric(arena, threshold=tanimoto_threshold)
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31 # Copy the results into the NumPy array.
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32 for row_index, row in enumerate(results.iter_indices_and_scores()):
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33 for target_index, target_score in row:
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34 similarities[row_index, target_index] = target_score
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36 # Return the distance matrix using the similarity matrix
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37 return 1.0 - similarities
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40 if __name__ == "__main__":
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41 parser = argparse.ArgumentParser(description="""NxN clustering for fps files.
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42 For more details please see the chemfp documentation:
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43 https://chemfp.readthedocs.org
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44 """)
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46 parser.add_argument("-i", "--input", dest="input_path",
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47 required=True,
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48 help="Path to the input file.")
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50 parser.add_argument("-c", "--cluster", dest="cluster_image",
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51 help="Path to the output cluster image.")
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53 parser.add_argument("-s", "--smatrix", dest="similarity_matrix",
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54 help="Path to the similarity matrix output file.")
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56 parser.add_argument("-t", "--threshold", dest="tanimoto_threshold",
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57 type=float, default=0.0,
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58 help="Tanimoto threshold [0.0]")
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60 parser.add_argument("--oformat", default='png', help="Output format (png, svg)")
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62 parser.add_argument('-p', '--processors', type=int,
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63 default=4)
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65 args = parser.parse_args()
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67 targets = chemfp.open( args.input_path, format='fps' )
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68 arena = chemfp.load_fingerprints( targets )
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69 distances = distance_matrix( arena, args.tanimoto_threshold )
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71 if args.similarity_matrix:
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72 distances.tofile( args.similarity_matrix )
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74 if args.cluster_image:
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75 linkage = hcluster.linkage( distances, method="single", metric="euclidean" )
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77 hcluster.dendrogram(linkage, labels=arena.ids)
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79 pylab.savefig( args.cluster_image, format=args.oformat )
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