Mercurial > repos > rnateam > graphclust_postprocessing
annotate evaluation.py @ 0:b797e13169a0 draft
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
| author | rnateam |
|---|---|
| date | Fri, 16 Dec 2016 07:34:49 -0500 |
| parents | |
| children | ed8c7191b322 |
| rev | line source |
|---|---|
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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1 import glob |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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2 from os import system |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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3 import re |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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4 |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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5 |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
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6 def sh(script): |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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7 system("bash -c '%s'" % script) |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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8 |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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9 |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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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
rnateam
parents:
diff
changeset
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11 listOfClusters = [] |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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12 listOfClasses = [] |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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13 cluster_seqs_stats_path = "RESULTS/*.cluster.all" |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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14 cluster_seqs_stats_files = glob.glob(cluster_seqs_stats_path) |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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15 |
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b797e13169a0
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 blackList = [] |
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b797e13169a0
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 numberOfClusters = 0 |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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18 for singleFile in sorted(cluster_seqs_stats_files): |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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19 numberOfClusters += 1 |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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20 with open(singleFile, "r") as f: |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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21 for line in f.readlines(): |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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22 uniqueId = line.split()[6] |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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23 clustNum = line.split()[1] |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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24 rnaClass, sep, tail = uniqueId.partition("_") |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
|
25 listOfClasses.append(rnaClass) |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
|
26 listOfClusters.append(clustNum) |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
|
27 with open(dataNames, "r") as names: |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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28 for line in names.readlines(): |
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b797e13169a0
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 fullUniqeId = line.split()[3] |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
|
30 rnaClass, sep, tail = fullUniqeId.partition("_") |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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31 short_unique = re.findall("_".join(["[^_]+"] * 2), fullUniqeId)[0] |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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32 if short_unique == uniqueId: |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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33 blackList.append(uniqueId) |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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34 |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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35 numberOfClusters += 1 # 1 cluster for all unassigned seqs |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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36 with open(dataNames, "r") as names: |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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37 for line in names.readlines(): |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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38 fullUniqeId = line.split()[3] |
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b797e13169a0
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 rnaClass, sep, tail = fullUniqeId.partition("_") |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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40 short_unique = re.findall("_".join(["[^_]+"] * 2), fullUniqeId)[0] |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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41 rnaClass, sep, tail = fullUniqeId.partition("_") |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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42 if short_unique not in blackList: |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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43 listOfClasses.append(rnaClass) |
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b797e13169a0
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 listOfClusters.append(str(numberOfClusters)) |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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45 numberOfClusters += 1 # separate cluster for all unassigned seqs |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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46 |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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47 toWrite = "" |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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48 for i in range(len(listOfClusters)): |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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49 toWrite += listOfClasses[i] + "\t" + listOfClusters[i] + '\n' |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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50 with open("RESULTS/fullTab.tabular", "w") as full: |
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b797e13169a0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff
changeset
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51 full.write(toWrite) |