annotate evaluation.py @ 0:4503c49f31c4 draft

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
author rnateam
date Fri, 16 Dec 2016 07:32:23 -0500
parents
children e166d1382033
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
1 import glob
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
2 from os import system
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
3 import re
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
4
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
5
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
6 def sh(script):
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
7 system("bash -c '%s'" % script)
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
8
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
9
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
10 dataNames = "FASTA/data.names"
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
11 listOfClusters = []
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
12 listOfClasses = []
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
13 cluster_seqs_stats_path = "RESULTS/*.cluster.all"
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
14 cluster_seqs_stats_files = glob.glob(cluster_seqs_stats_path)
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
15
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
16 blackList = []
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
17 numberOfClusters = 0
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
18 for singleFile in sorted(cluster_seqs_stats_files):
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
19 numberOfClusters += 1
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
20 with open(singleFile, "r") as f:
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
21 for line in f.readlines():
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
22 uniqueId = line.split()[6]
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
23 clustNum = line.split()[1]
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
24 rnaClass, sep, tail = uniqueId.partition("_")
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
25 listOfClasses.append(rnaClass)
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
26 listOfClusters.append(clustNum)
4503c49f31c4 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:
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
28 for line in names.readlines():
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
29 fullUniqeId = line.split()[3]
4503c49f31c4 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("_")
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
31 short_unique = re.findall("_".join(["[^_]+"] * 2), fullUniqeId)[0]
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
32 if short_unique == uniqueId:
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
33 blackList.append(uniqueId)
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
34
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
35 numberOfClusters += 1 # 1 cluster for all unassigned seqs
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
36 with open(dataNames, "r") as names:
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
37 for line in names.readlines():
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
38 fullUniqeId = line.split()[3]
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
39 rnaClass, sep, tail = fullUniqeId.partition("_")
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
40 short_unique = re.findall("_".join(["[^_]+"] * 2), fullUniqeId)[0]
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
41 rnaClass, sep, tail = fullUniqeId.partition("_")
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
42 if short_unique not in blackList:
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
43 listOfClasses.append(rnaClass)
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
44 listOfClusters.append(str(numberOfClusters))
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
45 numberOfClusters += 1 # separate cluster for all unassigned seqs
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
46
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
47 toWrite = ""
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
48 for i in range(len(listOfClusters)):
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
49 toWrite += listOfClasses[i] + "\t" + listOfClusters[i] + '\n'
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
50 with open("RESULTS/fullTab.tabular", "w") as full:
4503c49f31c4 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
diff changeset
51 full.write(toWrite)