annotate evaluation.py @ 14:98ceca65a0b6 draft

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 746497a64b955f6b9afc1944d1c1d8d877e53267
author rnateam
date Tue, 18 Jul 2017 01:41:51 -0400
parents b5f49453af8c
children 79df97a1bc0f
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b5f49453af8c planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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1 #!/usr/bin/env python2
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2 import glob
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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3 from os import system
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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4 import re
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5 from sklearn import metrics
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6 from shutil import make_archive
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8 def sh(script):
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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9 system("bash -c '%s'" % script)
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11 dataNames = "FASTA/data.names"
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13 listOfClusters = []
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14 listOfHeaders = []
b5f49453af8c planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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15 headersNames = set()
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16 cluster_seqs_stats_path = "RESULTS/*.cluster.all"
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17 cluster_seqs_stats_files = glob.glob(cluster_seqs_stats_path)
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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19 with open(dataNames, "r") as names:
b5f49453af8c planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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20 for line2 in names:
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21 splits2 = line2.split()
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22 fullHeader = ''
b5f49453af8c planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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23 if len(splits2) >= 6:
b5f49453af8c planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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24 fullHeader = splits2[5]
b5f49453af8c planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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25 headersNames.add(fullHeader)
b5f49453af8c planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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26
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27 blackList = []
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28 numberOfClusters = 0
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29 for singleFile in sorted(cluster_seqs_stats_files):
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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30 numberOfClusters += 1
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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31 with open(singleFile, "r") as f:
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32 for line in f:
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33 splits = line.split()
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34 header = ''
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35 if len(splits) >= 11:
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36 header = splits[10]
b5f49453af8c planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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37 clustNum = splits[2]
b5f49453af8c planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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38 listOfHeaders.append(header)
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39 listOfClusters.append(clustNum)
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40 if header in headersNames:
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41 blackList.append(header)
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43 numberOfClusters += 1 # 1 cluster for all unassigned seqs
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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44 with open(dataNames, "r") as names:
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45 for line in names.readlines():
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46 splits = line.split()
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47 fullUniqeId = splits[3]
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48 fullHeader = ''
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49 if len(splits) >= 6:
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50 fullHeader = line.split()[5]
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51 if fullHeader not in blackList or len(fullHeader) == 0:
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52 listOfHeaders.append(fullHeader)
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53 listOfClusters.append(str(numberOfClusters))
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54 numberOfClusters += 1 # separate cluster for all unassigned seqs
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56 toWrite = ""
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57 for i in range(len(listOfClusters)):
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58 toWrite += listOfHeaders[i] + "\t" + listOfClusters[i] + '\n'
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59 with open("RESULTS/fullTab.tabular", "w") as full:
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60 full.write(toWrite)
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63 pattern = re.compile("^RF.*$")
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64
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65 if len(listOfHeaders) > 1: # and pattern.match(str(listOfHeaders[0])):
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66
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67 completeness_score = metrics.completeness_score(listOfHeaders, listOfClusters)
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68 homogeneity_score = metrics.homogeneity_score(listOfHeaders, listOfClusters)
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69 adjusted_rand_score = metrics.adjusted_rand_score(listOfHeaders, listOfClusters)
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70 adjusted_mutual_info_score = metrics.adjusted_mutual_info_score(listOfHeaders, listOfClusters)
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71 v_measure_score = metrics.v_measure_score(listOfHeaders, listOfClusters)
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73 toWrite = "completeness_score : " + str(completeness_score) + "\n" + "homogeneity_score : " + str(homogeneity_score) + "\n" + "adjusted_rand_score : " +str(adjusted_rand_score) + "\n" + "adjusted_mutual_info_score : " + str(adjusted_mutual_info_score)+ "\n" + "v_measure_score : " + str(v_measure_score)
b8e32e577597 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 9bc3c9b613d106098a78e16534897c88a3738c07
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75 else:
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76 toWrite = "completeness_score : NA \nhomogeneity_score : NA \nadjusted_rand_score : NA \nadjusted_mutual_info_score : NA \nv_measure_score : NA"
b8e32e577597 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 9bc3c9b613d106098a78e16534897c88a3738c07
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78 with open("RESULTS/evaluation.txt", "w") as fOut:
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79 fOut.write(toWrite)
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80
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
rnateam
parents: 3
diff changeset
81
4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
rnateam
parents: 3
diff changeset
82 make_archive('RESULTS', 'zip', root_dir='RESULTS')