Mercurial > repos > rnateam > graphclust_postprocessing

annotate evaluation.py @ 9:08a3e826ccd7 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b8f82a8101d9eb74c8dbac51b8a0c75585a888a2
author rnateam
date Fri, 23 Feb 2018 10:47:01 -0500
parents 911e58500508
children a9965909555e
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911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents: 4
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1 #!/usr/bin/env python2
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4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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2 import glob
4503c49f31c4 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
4503c49f31c4 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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6c88ad83de28 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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5 from sklearn import metrics
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a8fde40f00fc planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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6 from shutil import make_archive
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08a3e826ccd7 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b8f82a8101d9eb74c8dbac51b8a0c75585a888a2
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7 import sys
08a3e826ccd7 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b8f82a8101d9eb74c8dbac51b8a0c75585a888a2
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8 import fnmatch, os
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10 def sh(script):
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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11 system("bash -c '%s'" % script)
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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12
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13 fasta_dir = sys.argv[1]
08a3e826ccd7 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b8f82a8101d9eb74c8dbac51b8a0c75585a888a2
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14 results_dir = sys.argv[2]
08a3e826ccd7 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b8f82a8101d9eb74c8dbac51b8a0c75585a888a2
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15 dataNames = fasta_dir+"/data.names"
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17 listOfClusters = []
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18 listOfHeaders = []
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19 headersNames = set()
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20 idsNames = set()
08a3e826ccd7 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b8f82a8101d9eb74c8dbac51b8a0c75585a888a2
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22
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23 names = os.listdir(results_dir)
08a3e826ccd7 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b8f82a8101d9eb74c8dbac51b8a0c75585a888a2
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24 cluster_seqs_stats_files = fnmatch.filter(names, '*.cluster.all')
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911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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25 with open(dataNames, "r") as names:
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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26 for line2 in names:
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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27 splits2 = line2.split()
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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28 fullHeader = ''
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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29 if len(splits2) >= 6:
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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30 fullHeader = splits2[5]
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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31 headersNames.add(fullHeader)
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32 fullID = splits2[3]
08a3e826ccd7 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b8f82a8101d9eb74c8dbac51b8a0c75585a888a2
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33 idsNames.add(fullID)
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34
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35 blackList = []
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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36 numberOfClusters = 0
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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37 for singleFile in sorted(cluster_seqs_stats_files):
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08a3e826ccd7 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b8f82a8101d9eb74c8dbac51b8a0c75585a888a2
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38 singleFile = os.path.join(results_dir,singleFile)
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39 numberOfClusters += 1
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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40 with open(singleFile, "r") as f:
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911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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41 for line in f:
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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42 splits = line.split()
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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43 header = ''
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44 idd = ''
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45 if len(splits) >= 11:
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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46 header = splits[10]
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47 idd = splits[8]
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48 clustNum = splits[2]
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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49 listOfHeaders.append(header)
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50 listOfClusters.append(clustNum)
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51 if idd in idsNames: #header in headersNames:
08a3e826ccd7 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b8f82a8101d9eb74c8dbac51b8a0c75585a888a2
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52 blackList.append(idd)
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54 numberOfClusters += 1 # 1 cluster for all unassigned seqs
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55 ignoreBlackList = False
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56 with open(dataNames, "r") as names:
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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57 for line in names.readlines():
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58 splits = line.split()
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59 fullUniqeId = splits[3]
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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60 fullHeader = ''
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61 fullID = ''
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62 if len(splits) >= 6:
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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63 fullHeader = line.split()[5]
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64 fullID = line.split()[3]
08a3e826ccd7 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit b8f82a8101d9eb74c8dbac51b8a0c75585a888a2
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65 if ignoreBlackList or ( fullID not in blackList #fullHeader not in blackList
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66 or len(fullHeader) == 0):
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67 listOfHeaders.append(fullHeader)
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68 listOfClusters.append(str(numberOfClusters))
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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69 numberOfClusters += 1 # separate cluster for all unassigned seqs
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70 # else:
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71 # print ("Skip header", fullHeader)
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73 toWrite = ""
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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74 for i in range(len(listOfClusters)):
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75 toWrite += listOfHeaders[i] + "\t" + listOfClusters[i] + '\n'
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77 with open(results_dir+"/fullTab.tabular", "w") as full:
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78 full.write(toWrite)
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81 pattern = re.compile("^RF.*$")
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82
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83 if len(listOfHeaders) > 1: # and pattern.match(str(listOfHeaders[0])):
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85 completeness_score = metrics.completeness_score(listOfHeaders, listOfClusters)
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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86 homogeneity_score = metrics.homogeneity_score(listOfHeaders, listOfClusters)
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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87 adjusted_rand_score = metrics.adjusted_rand_score(listOfHeaders, listOfClusters)
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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88 adjusted_mutual_info_score = metrics.adjusted_mutual_info_score(listOfHeaders, listOfClusters)
911e58500508 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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89 v_measure_score = metrics.v_measure_score(listOfHeaders, listOfClusters)
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91 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)
6c88ad83de28 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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92
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93
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94 else:
6c88ad83de28 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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95 toWrite = "completeness_score : NA \nhomogeneity_score : NA \nadjusted_rand_score : NA \nadjusted_mutual_info_score : NA \nv_measure_score : NA"
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96
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97 with open(os.path.join(results_dir,"evaluation.txt"), "w") as fOut:
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98 fOut.write(toWrite)
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100
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101 make_archive('RESULTS', 'zip', root_dir=results_dir)