Added correct wrapper to avoid calling module load from python script. Update...

Added correct wrapper to avoid calling module load from python script.  Update run_music.py script to correctly format final result data.

chipathlon/jobs/params/music_punctate.yaml

@@ -46,7 +46,7 @@ music_punctate:
     - name: scale_2216.bed
       type: file
       file_type: bed
-  command: run_music.py
+  command: music
   arguments:
     - "--prefix":
         type: string

chipathlon/jobs/scripts/run_music.py

@@ -22,8 +22,8 @@ peak_type_dict = {
     "broad": "-get_multiscale_broad_ERs"
 }
 
-subprocess.call(["/util/opt/lmod/lmod/init/profile"])
-subprocess.call(["module", "load", "music"])
+#subprocess.call(["/util/opt/lmod/lmod/init/profile"])
+#subprocess.call(["module", "load", "music"])
 
 if not os.path.isdir(args.prefix):
     # Create unqiue subdirectories for processing input
@@ -91,8 +91,17 @@ if not os.path.isdir(args.prefix):
             ], stdout=wh, stdin=sort.stdout)
         sort.wait()
 
-        shutil.copyfile("sorted_scale_%s_all.bed" % (scale,),
-            "../%s_sorted_scale_%s_all.bed" % (args.prefix, scale))
+        with open("sorted_scale_%s_all.bed" % (scale,), "r") as rh:
+            with open("../%s_sorted_scale_%s_all.bed" % (args.prefix, scale), "w") as wh:
+                for line in rh:
+                    info = line.split()
+                    # Score value shouldn't be negative
+                    info[4] = -1 * int(info[4])
+                    # pad columsn so there are actually 9
+                    for i in range(0, 3):
+                        info.append(0)
+                    # Write!
+                    wh.write(info.join("\t") + "\n")
 
 else:
     print "Directory %s already exists." % (args.prefix,)

chipathlon/jobs/wrappers/music_wrapper.sh

+#!/bin/bash
+
+. /util/opt/lmod/lmod/init/profile
+module load music
+
+run_music.py "$@"