Release version for Erange 4.0a

[erange.git] / test / testChksnp.py

diff --git a/test/testChksnp.py b/test/testChksnp.py
index b41fe659421377de86e576a7644abf9e8c5971b6..0fbbb7b2835ad2e7b8c52f38fdb4f116268444bc 100644 (file)
--- a/test/testChksnp.py
+++ b/test/testChksnp.py
@@ -23,6 +23,8 @@ class TestChksnp(unittest.TestCase):
 
     snpDB = "%s/dbSNP128.db" % dbPath
     altSnpDB = "%s/snp129cDNA.db" % dbPath
+    inputFileName = "testChkSNP_input.txt"
+    outputFileName = "testChkSNP_output.txt"
 
     def setUp(self):
         pass
@@ -33,8 +35,7 @@ class TestChksnp(unittest.TestCase):
 
 
     def testChkSNPFile(self):
-        inputFileName = "testChkSNP_input.txt"
-        infile = open(inputFileName, "w")
+        infile = open(self.inputFileName, "w")
         infile.write("# header line\n")
         snpEntry = string.join(["foo", "foo", "chr1", "691"], "\t")
         infile.write("%s\n" % snpEntry)
@@ -42,10 +43,8 @@ class TestChksnp(unittest.TestCase):
         infile.write("%s\n" % snpEntry)
         infile.close()
 
-        outputFileName = "testChkSNP_output.txt"
-
-        chksnp.chkSNPFile(self.snpDB, inputFileName, outputFileName)
-        outfile = open(outputFileName, "r")
+        chksnp.chkSNPFile(self.snpDB, self.inputFileName, self.outputFileName)
+        outfile = open(self.outputFileName, "r")
         line = outfile.readline()
         result = "foo\tfoo\tchr1\t691\trs10218492\tunknown\n"
         self.assertEquals(result, line)
@@ -53,10 +52,10 @@ class TestChksnp(unittest.TestCase):
         line = outfile.readline()
         self.assertEquals(result, line)
         outfile.close()
-        os.remove(outputFileName)
+        os.remove(self.outputFileName)
 
-        chksnp.chkSNPFile(self.snpDB, inputFileName, outputFileName, snpDBList=[self.altSnpDB])
-        outfile = open(outputFileName, "r")
+        chksnp.chkSNPFile(self.snpDB, self.inputFileName, self.outputFileName, snpDBList=[self.altSnpDB])
+        outfile = open(self.outputFileName, "r")
         line = outfile.readline()
         result = "foo\tfoo\tchr1\t691\trs10218492\tunknown\n"
         self.assertEquals(result, line)
@@ -65,13 +64,12 @@ class TestChksnp(unittest.TestCase):
         self.assertEquals(result, line)
         outfile.close()
 
-        os.remove(inputFileName)
-        os.remove(outputFileName)
+        os.remove(self.inputFileName)
+        os.remove(self.outputFileName)
 
 
     def testMain(self):
-        inputFileName = "testChkSNP_input.txt"
-        infile = open(inputFileName, "w")
+        infile = open(self.inputFileName, "w")
         infile.write("# header line\n")
         snpEntry = string.join(["foo", "foo", "chr1", "691"], "\t")
         infile.write("%s\n" % snpEntry)
@@ -79,11 +77,9 @@ class TestChksnp(unittest.TestCase):
         infile.write("%s\n" % snpEntry)
         infile.close()
 
-        outputFileName = "testChkSNP_output.txt"
-
-        argv = ["chksnp", self.snpDB, inputFileName, outputFileName]
+        argv = ["chksnp", self.snpDB, self.inputFileName, self.outputFileName]
         chksnp.main(argv)
-        outfile = open(outputFileName, "r")
+        outfile = open(self.outputFileName, "r")
         line = outfile.readline()
         result = "foo\tfoo\tchr1\t691\trs10218492\tunknown\n"
         self.assertEquals(result, line)
@@ -91,7 +87,10 @@ class TestChksnp(unittest.TestCase):
         line = outfile.readline()
         self.assertEquals(result, line)
         outfile.close()
-        os.remove(outputFileName)
+
+        os.remove(self.inputFileName)
+        os.remove(self.outputFileName)
+
 
     def testChkSNP(self):
         snpPropertiesList = []