Mercurial > repos > rmarenco > hubarchivecreator

diff BedSimpleRepeats.py @ 13:25809f699cb3 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 65ab931ef2b05a5acf06cbde3a746c94a0a0a4cb
author rmarenco
date Thu, 11 Aug 2016 19:02:29 -0400
parents d05236b15f81
children 3233451a3bd6
line wrap: on
line diff
--- a/BedSimpleRepeats.py	Wed Jul 27 10:43:58 2016 -0400
+++ b/BedSimpleRepeats.py	Thu Aug 11 19:02:29 2016 -0400
@@ -27,10 +27,14 @@
         # TODO: Change the name of the bb, to tool + genome + .bb
         trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) )
         myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
-        auto_sql_option = "%s%s" % ('-as=', os.path.join(self.tool_directory, 'trf_simpleRepeat.as'))
+
+        auto_sql_option = os.path.join(self.tool_directory, 'trf_simpleRepeat.as')
+
         with open(myBigBedFilePath, 'w') as bigBedFile:
-            subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name,
-                                 typeOption='-type=bed4+12',
+            subtools.bedToBigBed(sortedBedFile.name,
+                                 self.chromSizesFile.name,
+                                 bigBedFile.name,
+                                 typeOption='bed4+12',
                                  autoSql=auto_sql_option)
 
         # Create the Track Object