Mercurial > repos > bgruening > chemfp
comparison nxn_clustering.py @ 7:0d88631bb7de draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author | bgruening |
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date | Tue, 07 May 2019 13:32:50 -0400 |
parents | 70b071de9bee |
children | 198b1e30c739 |
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6:e3a7d6cc87af | 7:0d88631bb7de |
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67 targets = chemfp.open( args.input_path, format='fps' ) | 67 targets = chemfp.open( args.input_path, format='fps' ) |
68 arena = chemfp.load_fingerprints( targets ) | 68 arena = chemfp.load_fingerprints( targets ) |
69 distances = distance_matrix( arena, args.tanimoto_threshold ) | 69 distances = distance_matrix( arena, args.tanimoto_threshold ) |
70 | 70 |
71 if args.similarity_matrix: | 71 if args.similarity_matrix: |
72 distances.tofile( args.similarity_matrix ) | 72 numpy.savetxt(args.similarity_matrix, distances) |
73 | 73 |
74 if args.cluster_image: | 74 if args.cluster_image: |
75 linkage = hcluster.linkage( distances, method="single", metric="euclidean" ) | 75 linkage = hcluster.linkage(distances, method="single", metric="euclidean") |
76 hcluster.dendrogram(linkage, labels=arena.ids, leaf_rotation=90.) | |
77 pylab.savefig(args.cluster_image, format=args.oformat) | |
76 | 78 |
77 hcluster.dendrogram(linkage, labels=arena.ids) | |
78 | |
79 pylab.savefig( args.cluster_image, format=args.oformat ) | |
80 |