Mercurial > repos > rnateam > graphclust_postprocessing

comparison evaluation.py @ 0:b797e13169a0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
-1:000000000000 0:b797e13169a0
1 import glob
2 from os import system
3 import re
4
5
6 def sh(script):
7 system("bash -c '%s'" % script)
8
9
10 dataNames = "FASTA/data.names"
11 listOfClusters = []
12 listOfClasses = []
13 cluster_seqs_stats_path = "RESULTS/*.cluster.all"
14 cluster_seqs_stats_files = glob.glob(cluster_seqs_stats_path)
15
16 blackList = []
17 numberOfClusters = 0
18 for singleFile in sorted(cluster_seqs_stats_files):
19 numberOfClusters += 1
20 with open(singleFile, "r") as f:
21 for line in f.readlines():
22 uniqueId = line.split()[6]
23 clustNum = line.split()[1]
24 rnaClass, sep, tail = uniqueId.partition("_")
25 listOfClasses.append(rnaClass)
26 listOfClusters.append(clustNum)
27 with open(dataNames, "r") as names:
28 for line in names.readlines():
29 fullUniqeId = line.split()[3]
30 rnaClass, sep, tail = fullUniqeId.partition("_")
31 short_unique = re.findall("_".join(["[^_]+"] * 2), fullUniqeId)[0]
32 if short_unique == uniqueId:
33 blackList.append(uniqueId)
34
35 numberOfClusters += 1 # 1 cluster for all unassigned seqs
36 with open(dataNames, "r") as names:
37 for line in names.readlines():
38 fullUniqeId = line.split()[3]
39 rnaClass, sep, tail = fullUniqeId.partition("_")
40 short_unique = re.findall("_".join(["[^_]+"] * 2), fullUniqeId)[0]
41 rnaClass, sep, tail = fullUniqeId.partition("_")
42 if short_unique not in blackList:
43 listOfClasses.append(rnaClass)
44 listOfClusters.append(str(numberOfClusters))
45 numberOfClusters += 1 # separate cluster for all unassigned seqs
46
47 toWrite = ""
48 for i in range(len(listOfClusters)):
49 toWrite += listOfClasses[i] + "\t" + listOfClusters[i] + '\n'
50 with open("RESULTS/fullTab.tabular", "w") as full:
51 full.write(toWrite)