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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
snpDB = "%s/dbSNP128.db" % dbPath
altSnpDB = "%s/snp129cDNA.db" % dbPath
+ inputFileName = "testChkSNP_input.txt"
+ outputFileName = "testChkSNP_output.txt"
def setUp(self):
pass
def setUp(self):
pass
@@
-33,8
+35,7
@@
class TestChksnp(unittest.TestCase):
def testChkSNPFile(self):
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)
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()
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)
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()
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)
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()
self.assertEquals(result, line)
outfile.close()
- os.remove(inputFileName)
- os.remove(outputFileName)
+ os.remove(
self.
inputFileName)
+ os.remove(
self.
outputFileName)
def testMain(self):
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)
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()
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)
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)
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()
line = outfile.readline()
self.assertEquals(result, line)
outfile.close()
- os.remove(outputFileName)
+
+ os.remove(self.inputFileName)
+ os.remove(self.outputFileName)
+
def testChkSNP(self):
snpPropertiesList = []
def testChkSNP(self):
snpPropertiesList = []