Mercurial > repos > zzhou > bamedit

diff bamedit.py @ 31:925fe134e569 draft

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Uploaded
author zzhou
date Mon, 26 Nov 2012 11:40:12 -0500
parents 903000ebc92c
children df4eb276977e
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--- a/bamedit.py	Mon Nov 26 11:36:38 2012 -0500
+++ b/bamedit.py	Mon Nov 26 11:40:12 2012 -0500
@@ -13,8 +13,8 @@
 def main():
     options = simplejson.load( open( sys.argv[1] ) )
 
-    shscript = "$SCRIPT_PATH/split.sh"
-    plscript = "$SCRIPT_PATH/pileup.pl"
+    shscript = "%s/split.sh" % os.environ.get('SCRIPT_PATH')
+    plscript = "%s/pileup.pl" % os.environ.get('SCRIPT_PATH')
     print shscript
     if(options['action'] == "merge"):
 	cmdline = "samtools merge  %s %s %s" % ( options['bamout'], options['input1'], options['input2'] )