Mercurial > repos > rnateam > graphclust_cmfinder
diff cmFinder.py @ 0:78772eedd780 draft
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 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cmFinder.py Fri Dec 16 07:34:34 2016 -0500 @@ -0,0 +1,43 @@ +import os +import sys +from shutil import copyfile +from os import system + + +def sh(script): + system("bash -c '%s'" % script) + + +model_tree_stk = sys.argv[1] +cmfinder_fa = sys.argv[2] +path = sys.argv[3] + +gapCmd = "" +gapVal = "" +if len(sys.argv) > 4: + gapCmd = sys.argv[4] + gapVal = sys.argv[5] + + +cmd = " cp -f %s model.cmfinder.stk" % (model_tree_stk) +sh(cmd) + +alifoldCmd = "%salifold.pl -file %s" % (path, model_tree_stk) +# alifoldCmd = "perl " + path + "/alifold.pl -file " + model_tree_stk +sh(alifoldCmd) + +cmd_stk = "%smloc2stockholm.pl -file model.cmfinder.stk -split_input yes --con_struct %s.alifold" % (path, model_tree_stk) +# cmd_stk = "perl " + path + "/mloc2stockholm.pl -file model.cmfinder.stk -split_input yes --con_struct " + model_tree_stk + ".alifold" +sh(cmd_stk) + +model_tree_stk_sth = "model.cmfinder.stk.sth" +x = "cat " + model_tree_stk_sth +sh("mv model.cmfinder.stk.sth model.tree.stk") + +sh("cmfinder %s %s -a model.tree.stk %s output > model.cmfinder.stk" % (gapCmd, gapVal, cmfinder_fa)) +# sh("cmfinder " + gapCmd + " " + gapVal + " -a model.tree.stk" + " " + cmfinder_fa + " " + " output > model.cmfinder.stk") + +if os.path.isfile('output'): + sh("rm output") +else: + copyfile("model.tree.stk", "model.cmfinder.stk")