Mercurial > repos > rnateam > graphclust_postprocessing

annotate evaluation.py @ 5:4310ac018d05 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author rnateam
date Sat, 21 Jan 2017 17:39:21 -0500
parents 79b9117aef01
children 869a6e807d76
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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1 import glob
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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2 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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3 import re
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b8e32e577597 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 9bc3c9b613d106098a78e16534897c88a3738c07
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4 from sklearn import metrics
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4310ac018d05 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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5 from shutil import make_archive
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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7 def sh(script):
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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8 system("bash -c '%s'" % script)
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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10 dataNames = "FASTA/data.names"
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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12 listOfClusters = []
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13 listOfClasses = []
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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14 cluster_seqs_stats_path = "RESULTS/*.cluster.all"
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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15 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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17 blackList = []
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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18 numberOfClusters = 0
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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19 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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20 numberOfClusters += 1
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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21 with open(singleFile, "r") as f:
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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22 for line in f.readlines():
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23 uniqueId = line.split()[7]
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24 clustNum = line.split()[1]
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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25 rnaClass, sep, tail = uniqueId.partition("_")
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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26 listOfClasses.append(rnaClass)
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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27 listOfClusters.append(clustNum)
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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28 with open(dataNames, "r") as names:
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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29 for line in names.readlines():
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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30 fullUniqeId = line.split()[3]
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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31 rnaClass, sep, tail = fullUniqeId.partition("_")
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32 if fullUniqeId == uniqueId:
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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33 blackList.append(uniqueId)
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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35 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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36 with open(dataNames, "r") as names:
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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37 for line in names.readlines():
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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38 fullUniqeId = line.split()[3]
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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39 rnaClass, sep, tail = fullUniqeId.partition("_")
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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40 rnaClass, sep, tail = fullUniqeId.partition("_")
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41 if fullUniqeId not in blackList:
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b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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42 listOfClasses.append(rnaClass)
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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43 listOfClusters.append(str(numberOfClusters))
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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44 numberOfClusters += 1 # separate 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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46 toWrite = ""
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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47 for i in range(len(listOfClusters)):
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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48 toWrite += listOfClasses[i] + "\t" + listOfClusters[i] + '\n'
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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49 with open("RESULTS/fullTab.tabular", "w") as full:
b797e13169a0 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
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50 full.write(toWrite)
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53 pattern = re.compile("^RF.*$")
b8e32e577597 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 9bc3c9b613d106098a78e16534897c88a3738c07
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56 if len(listOfClasses) > 0 and pattern.match(str(listOfClasses[0])):
b8e32e577597 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 9bc3c9b613d106098a78e16534897c88a3738c07
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58 completeness_score = metrics.completeness_score(listOfClasses, listOfClusters)
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59 homogeneity_score = metrics.homogeneity_score(listOfClasses, listOfClusters)
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60 adjusted_rand_score = metrics.adjusted_rand_score(listOfClasses, listOfClusters)
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61 adjusted_mutual_info_score = metrics.adjusted_mutual_info_score(listOfClasses, listOfClusters)
b8e32e577597 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 9bc3c9b613d106098a78e16534897c88a3738c07
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62 v_measure_score = metrics.v_measure_score(listOfClasses, listOfClusters)
b8e32e577597 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 9bc3c9b613d106098a78e16534897c88a3738c07
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64 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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66 else:
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67 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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69 with open("RESULTS/evaluation.txt", "w") as fOut:
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70 fOut.write(toWrite)
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73 make_archive('RESULTS', 'zip', root_dir='RESULTS')