Mercurial > repos > rnateam > graphclust_cmfinder

comparison cmFinder.py @ 0:78772eedd780 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit 21aaee40723b5341b4236edeb0e72995c2054053
author rnateam
date Fri, 16 Dec 2016 07:34:34 -0500
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-1:000000000000 0:78772eedd780
1 import os
2 import sys
3 from shutil import copyfile
4 from os import system
5
6
7 def sh(script):
8 system("bash -c '%s'" % script)
9
10
11 model_tree_stk = sys.argv[1]
12 cmfinder_fa = sys.argv[2]
13 path = sys.argv[3]
14
15 gapCmd = ""
16 gapVal = ""
17 if len(sys.argv) > 4:
18 gapCmd = sys.argv[4]
19 gapVal = sys.argv[5]
20
21
22 cmd = " cp -f %s model.cmfinder.stk" % (model_tree_stk)
23 sh(cmd)
24
25 alifoldCmd = "%salifold.pl -file %s" % (path, model_tree_stk)
26 # alifoldCmd = "perl " + path + "/alifold.pl -file " + model_tree_stk
27 sh(alifoldCmd)
28
29 cmd_stk = "%smloc2stockholm.pl -file model.cmfinder.stk -split_input yes --con_struct %s.alifold" % (path, model_tree_stk)
30 # cmd_stk = "perl " + path + "/mloc2stockholm.pl -file model.cmfinder.stk -split_input yes --con_struct " + model_tree_stk + ".alifold"
31 sh(cmd_stk)
32
33 model_tree_stk_sth = "model.cmfinder.stk.sth"
34 x = "cat " + model_tree_stk_sth
35 sh("mv model.cmfinder.stk.sth model.tree.stk")
36
37 sh("cmfinder %s %s -a model.tree.stk %s output > model.cmfinder.stk" % (gapCmd, gapVal, cmfinder_fa))
38 # sh("cmfinder " + gapCmd + " " + gapVal + " -a model.tree.stk" + " " + cmfinder_fa + " " + " output > model.cmfinder.stk")
39
40 if os.path.isfile('output'):
41 sh("rm output")
42 else:
43 copyfile("model.tree.stk", "model.cmfinder.stk")