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annotate pca_cosine.py @ 2:795a5996cdc8 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 19:40:30 +0000
parents 78aa3659fcd1
children
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78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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1 #!/usr/bin/env python
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78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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3 import argparse
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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4 import csv
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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5 import sys
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7 import MDAnalysis as mda
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8 import MDAnalysis.analysis.pca as pca
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10 import numpy as np
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13 def parse_command_line(argv):
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14 parser = argparse.ArgumentParser()
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15 parser.add_argument('--itraj', help='input traj')
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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16 parser.add_argument('--istr', help='input str')
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17 parser.add_argument('--itrajext', help='input traj ext')
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18 parser.add_argument('--istrext', help='input str ext')
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19 parser.add_argument('--icomponents', help='number of principle components')
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20 parser.add_argument('--iindex', help='index of the PC')
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21 parser.add_argument('--output', help='output')
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22 parser.add_argument('--cosout', help='cosine output')
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23 return parser.parse_args()
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26 args = parse_command_line(sys.argv)
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28 u = mda.Universe(args.istr, args.itraj,
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29 topology_format=args.istrext, format=args.itrajext)
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31 components = int(args.icomponents)
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32 pca_index = int(args.iindex)
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34 PSF_pca = pca.PCA(u, select='backbone')
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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35 PSF_pca.run()
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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36 n_pcs = np.where(PSF_pca.cumulated_variance > 0.95)[0][0]
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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37 atomgroup = u.select_atoms('backbone')
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39 pca_space = PSF_pca.transform(atomgroup, n_components=components)
78aa3659fcd1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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40 cosine = mda.analysis.pca.cosine_content(pca_space, pca_index)
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42 PCA = list(pca_space)
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44 with open(args.output, 'w') as f:
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45 writer = csv.writer(f, delimiter='\t')
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46 writer.writerows(PCA)
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48 with open(args.cosout, 'w') as f1:
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49 f1.write(str(cosine))