Mercurial > repos > zzhou > bamedit

changeset 52:14b64c3d3250 draft

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Uploaded
author zzhou
date Mon, 26 Nov 2012 13:59:12 -0500
parents 0e5d77e4d9bf
children 19dfa6847218
files bamedit.py
diffstat 1 files changed, 5 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/bamedit.py	Mon Nov 26 13:56:54 2012 -0500
+++ b/bamedit.py	Mon Nov 26 13:59:12 2012 -0500
@@ -14,21 +14,19 @@
    options = simplejson.load( open( sys.argv[1] ) )
 
 
-   shscript = "%s/pileup.pl" % os.environ.get('SCRIPT_PATH')
-   plscript = "%s/pileup.pl" % os.environ.get('SCRIPT_PATH')
-   print plscript 
+   shscript = "%s/split.sh" % os.environ.get('SCRIPT_PATH')
+   print shscript
+   testing = sys.argv[2]
+   print testing
    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'] )
-        asdf = options['asdf']
-        print asdf
 	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 %s %s %s %s %s %s" % ( plscript, options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] )
+	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'] )
     elif (options['action'] == "filter"):
 	cmdline = "samtools view -q %s %s -bo %s" % ( options['quality'], options['input1'], options['bamout'] )