erange version 4.0a dev release

[erange.git] / test / testGeneMrnaCounts.py

diff --git a/test/testGeneMrnaCounts.py b/test/testGeneMrnaCounts.py
index 62f1649d8cb27be429c8b56e41c9c4a5a674eeba..4f2ea083dbfbc3034a72afcaff99896dddfe8cce 100644 (file)
--- a/test/testGeneMrnaCounts.py
+++ b/test/testGeneMrnaCounts.py
@@ -12,10 +12,10 @@ Located feature 728439 by:
 '''
 import unittest
 import os
-from Erange import geneMrnaCounts
+from erange import geneMrnaCounts
 from cistematic.core.geneinfo import geneinfoDB
 from cistematic.genomes import Genome
-from Erange.commoncode import readDataset
+from erange import ReadDataset
 
 
 class TestGeneMrnaCounts(unittest.TestCase):
@@ -25,7 +25,7 @@ class TestGeneMrnaCounts(unittest.TestCase):
     outfilename = "testGeneMrnaCounts.txt"
 
     def setUp(self):
-        self.rds = readDataset(self.testDBName, initialize=True, datasetType="RNA", verbose=False)
+        self.rds = ReadDataset.ReadDataset(self.testDBName, initialize=True, datasetType="RNA", verbose=False)
 
 
     def tearDown(self):
@@ -66,7 +66,7 @@ class TestGeneMrnaCounts(unittest.TestCase):
 
         outfile.close()
         os.remove(self.outfilename)
-        reads = self.rds.getReadsDict(withFlag=True, entryDict=True)
+        reads = self.rds.getReadsDict(withFlag=True)
         self.assertEquals("728439", reads["1"][0]["flag"])
 
         geneMrnaCounts.geneMrnaCounts(self.genomeName, self.testDBName, self.outfilename,
@@ -80,7 +80,7 @@ class TestGeneMrnaCounts(unittest.TestCase):
 
         outfile.close()
         os.remove(self.outfilename)
-        reads = self.rds.getReadsDict(withFlag=True, entryDict=True)
+        reads = self.rds.getReadsDict(withFlag=True)
         self.assertEquals("728439", reads["1"][0]["flag"])