Mercurial > repos > rnateam > graphclust_postprocessing
annotate evaluation.py @ 7:911e58500508 draft
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
| author | rnateam |
|---|---|
| date | Wed, 31 May 2017 15:02:00 -0400 |
| parents | dbcea781900e |
| children | 08a3e826ccd7 |
| rev | line source |
|---|---|
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7
911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
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changeset
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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
rnateam
parents:
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2 import glob |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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3 from os import system |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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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
rnateam
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5 from sklearn import metrics |
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3
a8fde40f00fc
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
rnateam
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6 from shutil import make_archive |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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7 |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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8 def sh(script): |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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9 system("bash -c '%s'" % script) |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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10 |
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1
e166d1382033
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9
rnateam
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11 dataNames = "FASTA/data.names" |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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12 |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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changeset
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13 listOfClusters = [] |
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7
911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
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diff
changeset
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14 listOfHeaders = [] |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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15 headersNames = set() |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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16 cluster_seqs_stats_path = "RESULTS/*.cluster.all" |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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17 cluster_seqs_stats_files = glob.glob(cluster_seqs_stats_path) |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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18 |
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7
911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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19 with open(dataNames, "r") as names: |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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20 for line2 in names: |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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21 splits2 = line2.split() |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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22 fullHeader = '' |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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23 if len(splits2) >= 6: |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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24 fullHeader = splits2[5] |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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25 headersNames.add(fullHeader) |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
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26 |
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0
4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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27 blackList = [] |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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changeset
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28 numberOfClusters = 0 |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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29 for singleFile in sorted(cluster_seqs_stats_files): |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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30 numberOfClusters += 1 |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
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31 with open(singleFile, "r") as f: |
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7
911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
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32 for line in f: |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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33 splits = line.split() |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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34 header = '' |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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35 if len(splits) >= 11: |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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36 header = splits[10] |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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37 clustNum = splits[2] |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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38 listOfHeaders.append(header) |
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0
4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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39 listOfClusters.append(clustNum) |
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7
911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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40 if header in headersNames: |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
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41 blackList.append(header) |
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0
4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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42 |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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43 numberOfClusters += 1 # 1 cluster for all unassigned seqs |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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44 with open(dataNames, "r") as names: |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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45 for line in names.readlines(): |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
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46 splits = line.split() |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
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diff
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47 fullUniqeId = splits[3] |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
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48 fullHeader = '' |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
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49 if len(splits) >= 6: |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
changeset
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50 fullHeader = line.split()[5] |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
4
diff
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51 if fullHeader not in blackList or len(fullHeader) == 0: |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
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diff
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52 listOfHeaders.append(fullHeader) |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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53 listOfClusters.append(str(numberOfClusters)) |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
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54 numberOfClusters += 1 # separate cluster for all unassigned seqs |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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55 |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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56 toWrite = "" |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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57 for i in range(len(listOfClusters)): |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
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58 toWrite += listOfHeaders[i] + "\t" + listOfClusters[i] + '\n' |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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59 with open("RESULTS/fullTab.tabular", "w") as full: |
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4503c49f31c4
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
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60 full.write(toWrite) |
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6c88ad83de28
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
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61 |
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6c88ad83de28
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
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62 |
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6c88ad83de28
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
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63 pattern = re.compile("^RF.*$") |
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6c88ad83de28
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
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64 |
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7
911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
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65 if len(listOfHeaders) > 1: # and pattern.match(str(listOfHeaders[0])): |
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6c88ad83de28
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
parents:
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66 |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
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67 completeness_score = metrics.completeness_score(listOfHeaders, listOfClusters) |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
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68 homogeneity_score = metrics.homogeneity_score(listOfHeaders, listOfClusters) |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
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69 adjusted_rand_score = metrics.adjusted_rand_score(listOfHeaders, listOfClusters) |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
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70 adjusted_mutual_info_score = metrics.adjusted_mutual_info_score(listOfHeaders, listOfClusters) |
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911e58500508
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 65d322f9ab2f24d65b307f3553589149a1d678d5
rnateam
parents:
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71 v_measure_score = metrics.v_measure_score(listOfHeaders, listOfClusters) |
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6c88ad83de28
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
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72 |
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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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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) |
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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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74 |
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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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75 else: |
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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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76 toWrite = "completeness_score : NA \nhomogeneity_score : NA \nadjusted_rand_score : NA \nadjusted_mutual_info_score : NA \nv_measure_score : NA" |
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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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77 |
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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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78 with open("RESULTS/evaluation.txt", "w") as fOut: |
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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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79 fOut.write(toWrite) |
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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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80 |
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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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81 |
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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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82 make_archive('RESULTS', 'zip', root_dir='RESULTS') |