Mercurial > repos > rnateam > graphclust_postprocessing_no_align

annotate evaluation.py @ 0:0a48b2db75e7 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
author rnateam
date Sat, 27 Oct 2018 13:49:00 -0400
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0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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1 #!/usr/bin/env python
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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2 import glob
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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3 from os import system
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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4 import re
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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5 from sklearn import metrics
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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6 from shutil import make_archive
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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7 import sys
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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8 import fnmatch, os
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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9
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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10 def sh(script):
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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11 system("bash -c '%s'" % script)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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12
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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13 fasta_dir = sys.argv[1]
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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14 results_dir = sys.argv[2]
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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15 dataNames = os.path.join(fasta_dir,"data.names")
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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16
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17 listOfClusters = []
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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18 listOfHeaders = []
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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19 headersNames = set()
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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20 idsNames = set()
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21
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22
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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23 names = os.listdir(results_dir)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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24 cluster_seqs_stats_files = fnmatch.filter(names, '*.cluster.all')
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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25 with open(dataNames, "r") as names:
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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26 for line2 in names:
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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27 splits2 = line2.split()
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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28 fullHeader = ''
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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29 if len(splits2) >= 6:
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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30 fullHeader = splits2[5]
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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31 headersNames.add(fullHeader)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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32 fullID = splits2[3]
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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33 idsNames.add(fullID)
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34
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35 blackList = []
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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36 numberOfClusters = 0
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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37 for singleFile in sorted(cluster_seqs_stats_files):
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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38 singleFile = os.path.join(results_dir,singleFile)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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39 numberOfClusters += 1
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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40 with open(singleFile, "r") as f:
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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41 for line in f:
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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42 splits = line.split()
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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43 header = ''
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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44 idd = ''
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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45 if len(splits) >= 11:
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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46 header = splits[10]
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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47 idd = splits[8]
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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48 clustNum = splits[2]
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49 listOfHeaders.append(header)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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50 listOfClusters.append(clustNum)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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51 if idd in idsNames: #header in headersNames:
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52 blackList.append(idd)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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53
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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54 numberOfClusters += 1 # 1 cluster for all unassigned seqs
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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55 ignoreBlackList = False
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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56 with open(dataNames, "r") as names:
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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57 for line in names:
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58 splits = line.split()
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59 fullUniqeId = splits[3]
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60 fullHeader = ''
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61 fullID = ''
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62 if len(splits) >= 6:
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63 fullHeader = line.split()[5]
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64 fullID = line.split()[3]
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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))
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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69 numberOfClusters += 1 # separate cluster for all unassigned seqs
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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70 # else:
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71 # print ("Skip header", fullHeader)
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72
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73 toWrite = ""
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74 for i in range(len(listOfClusters)):
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75 toWrite += "%s\t%s\n" % (listOfHeaders[i], listOfClusters[i])
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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76
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77 with open(os.path.join(results_dir,"fullTab.tabular"), "w") as full:
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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78 full.write(toWrite)
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79
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80
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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])):
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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84
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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85 completeness_score = metrics.completeness_score(listOfHeaders, listOfClusters)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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86 homogeneity_score = metrics.homogeneity_score(listOfHeaders, listOfClusters)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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87 adjusted_rand_score = metrics.adjusted_rand_score(listOfHeaders, listOfClusters)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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88 adjusted_mutual_info_score = metrics.adjusted_mutual_info_score(listOfHeaders, listOfClusters)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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89 v_measure_score = metrics.v_measure_score(listOfHeaders, listOfClusters)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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90
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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91 toWrite = "completeness_score : {}\n".format(completeness_score)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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92 toWrite += "homogeneity_score : {}\n".format(homogeneity_score)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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93 toWrite += "adjusted_rand_score : {}\n".format(adjusted_rand_score)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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94 toWrite += "adjusted_mutual_info_score : {}\n".format(adjusted_mutual_info_score)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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95 toWrite += "v_measure_score : {}\n".format(v_measure_score)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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96
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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97
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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98 else:
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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99 toWrite = "completeness_score : NA \nhomogeneity_score : NA \nadjusted_rand_score : NA \nadjusted_mutual_info_score : NA \nv_measure_score : NA"
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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100
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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101 with open(os.path.join(results_dir,"evaluation.txt"), "w") as fOut:
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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102 fOut.write(toWrite)
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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103
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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104
0a48b2db75e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e
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105 make_archive('RESULTS', 'zip', root_dir=results_dir)