484b2937518ba7c87d091637ecda30fa7ef0d890
wong
  Wed Nov 2 18:12:45 2011 -0700
made it so that it first checks with trackDb.wgEncode.ra to try and determine an alpha track.ra file
diff --git python/lib/ucscgenomics/track.py python/lib/ucscgenomics/track.py
index e8e5085..831c10f 100644
--- python/lib/ucscgenomics/track.py
+++ python/lib/ucscgenomics/track.py
@@ -296,37 +296,41 @@
         organisms = {
             'hg19': 'human',
             'hg18': 'human',
             'mm9': 'mouse',
             'encodeTest': 'human'
         }
         
         if database in organisms:
             self._organism = organisms[database]
         else:
             raise KeyError(database + ' is not a valid database')
         
         if not self._trackPath.endswith('/'):
             self._trackPath = self._trackPath + '/'
         
-        self._trackDbPath = self._trackPath + self._organism + '/' + database + '/' + compositeName + '.ra'
+        #self._trackDbPath = self._trackPath + self._organism + '/' + database + '/' + compositeName + '.ra'
         self._trackDbDir = self._trackPath + self._organism + '/' + database + '/'
-        if not os.path.isfile(self._trackDbPath):
-            raise KeyError(self._trackDbPath + ' does not exist')
+        
         
         
         
         self._alphaMdbPath = self._trackPath + self._organism + '/' + database + '/metaDb/alpha/' + mdbCompositeName + '.ra'
         self._betaMdbPath = self._trackPath + self._organism + '/' + database + '/metaDb/beta/' + mdbCompositeName + '.ra'    
         self._publicMdbPath = self._trackPath + self._organism + '/' + database + '/metaDb/public/' + mdbCompositeName + '.ra'
         self._alphaMdbDir = self._trackPath + self._organism + '/' + database + '/metaDb/alpha/'
         self._betaMdbDir = self._trackPath + self._organism + '/' + database + '/metaDb/beta/'
         self._publicMdbDir = self._trackPath + self._organism + '/' + database + '/metaDb/public/'
         self._downloadsDirectory = '/hive/groups/encode/dcc/analysis/ftp/pipeline/' + database + '/' + compositeName + '/'
         self._httpDownloadsPath = '/usr/local/apache/htdocs-hgdownload/goldenPath/' + database + '/encodeDCC/' + compositeName + '/'
         self._rrHttpDir = '/usr/local/apache/htdocs/goldenPath/' + database + '/encodeDCC/' + compositeName + '/'
         self._notesDirectory = os.path.expanduser("~/kent/src/hg/makeDb/doc/encodeDcc%s" % database.capitalize()) + '/'
         self._url = 'http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=' + database + '&g=' + compositeName
         self._database = database
         self._name = compositeName        
         self._md5path = '/hive/groups/encode/dcc/analysis/ftp/pipeline/' + database + '/' + compositeName + '/md5sum.txt'
+        self._trackDbPath = self.currentTrackDb
+        if self._trackDbPath == None:
+            self._trackDbPath = self._trackPath + self._organism + '/' + database + '/' + compositeName + '.ra' 
+        if not os.path.isfile(self._trackDbPath):
+            raise KeyError(self._trackDbPath + ' does not exist')