diff bamedit.py @ 30:903000ebc92c draft

Uploaded

--- a/bamedit.py	Mon Nov 26 11:33:11 2012 -0500
+++ b/bamedit.py	Mon Nov 26 11:36:38 2012 -0500
@@ -13,16 +13,19 @@
 def main():
     options = simplejson.load( open( sys.argv[1] ) )
 
+    shscript = "$SCRIPT_PATH/split.sh"
+    plscript = "$SCRIPT_PATH/pileup.pl"
+    print shscript
     if(options['action'] == "merge"):
 	cmdline = "samtools merge  %s %s %s" % ( options['bamout'], options['input1'], options['input2'] )
 	if('input3' in options):
 		cmdline = "samtools merge  %s %s %s %s" % ( options['bamout'], options['input1'], options['input2'], options['input3'] )
     elif (options['action'] == "split"):
 	#cmdline = "bash /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC/bamedit/split.sh %s %s %s" % ( options['bamout'], options['bamout2'], options['input1'] )
-	cmdline = "bash $SCRIPT_PATH\/split.sh %s %s %s" % ( options['bamout'], options['bamout2'], options['input1'] )
+	cmdline = "bash %s %s %s %s" % ( shscript, options['bamout'], options['bamout2'], options['input1'] )
     elif (options['action'] == "pileup"):
 	#cmdline = "perl /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC/bamedit/pileup.pl %s %s %s %s %s" % ( options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] )
-	cmdline = "perl $SCRIPT_PATH\/pileup.pl %s %s %s %s %s" % ( options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] )
+	cmdline = "perl %s %s %s %s %s %s" % ( plscript, options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] )
     elif (options['action'] == "filter"):
 	cmdline = "samtools view -q %s %s -bo %s" % ( options['quality'], options['input1'], options['bamout'] )