3ee949f62ece9f74180d5a25721f66ecc0948ac0
wong
  Tue Oct 25 16:59:14 2011 -0700
added in ability to use a custom mdb
diff --git python/lib/ucscgenomics/track.py python/lib/ucscgenomics/track.py
index 98d4053..2cbd0da 100644
--- python/lib/ucscgenomics/track.py
+++ python/lib/ucscgenomics/track.py
@@ -261,56 +261,62 @@
         return self._organism
     @property
     def currentTrackDb(self):
         trackDb = self._trackDbDir + "trackDb.wgEncode.ra"
         f = open(trackDb, "r")
         lines = f.readlines()
         p = re.compile(".*(%s\S+) ?(\S+)" % self._name)
         for i in lines:
             m = p.match(i)
             if m and re.search('alpha', m.group(2)):
                 tdbpath = "%s%s" % (self._trackDbDir, m.group(1))
                 return tdbpath
         return None
 
  
-    def __init__(self, database, compositeName, trackPath=None):
+    def __init__(self, database, compositeName, trackPath=None, mdbCompositeName=None):
+        
+        if mdbCompositeName == None:
+            mdbCompositeName = compositeName
         
         if trackPath == None:
             self._trackPath = os.path.expanduser('~/kent/src/hg/makeDb/trackDb/')
         else:
             self._trackPath = trackPath
             
         organisms = {
             'hg19': 'human',
             'hg18': 'human',
-            'mm9': 'mouse'
+            '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._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/' + compositeName + '.ra'
-        self._betaMdbPath = self._trackPath + self._organism + '/' + database + '/metaDb/beta/' + compositeName + '.ra'    
-        self._publicMdbPath = self._trackPath + self._organism + '/' + database + '/metaDb/public/' + compositeName + '.ra'
+        
+        
+        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'