Merge branch 'stable-1.x' into bloody

CHANGELOG.rst

@@ -1,3 +1,9 @@
+1.1.7
+=====
+
+* BUG FIX: looping through CSV lines now works
+* Added tests for CSV
+
 1.1.6
 =====
 

pyGeno/pyGenoObjectBases.py

@@ -198,7 +198,7 @@ def flushIndexes(cls) :
 	def help(cls) :
 		"""Returns a list of available field for queries. Ex 
 		Transcript.help()"""
-		return cls._wrapped_class.help()
+		return cls._wrapped_class.help().replace("_Raba", "")
 
 	@classmethod
 	def ensureGlobalIndex(cls, fields) :

pyGeno/tests/csv_tests.py

@@ -0,0 +1,32 @@
+import unittest
+from pyGeno.tools.parsers.CSVTools import *
+
+class CSVTests(unittest.TestCase):
+
+	def setUp(self):
+		pass
+
+	def tearDown(self):
+		pass
+
+	def test_createParse(self) :
+		testVals = ["test", "test2"]
+		c = CSVFile(legend = ["col1", "col2"], separator = "\t")
+		l = c.newLine()
+		l["col1"] = testVals[0]
+		l = c.newLine()
+		l["col1"] = testVals[1]
+		c.save("test.csv")
+
+		c2 = CSVFile()
+		c2.parse("test.csv", separator = "\t")
+		i = 0
+		for l in c2 :
+			self.assertEqual(l["col1"], testVals[i])
+			i += 1
+
+def runTests() :
+	unittest.main()
+
+if __name__ == "__main__" :
+	runTests()

pyGeno/tests/tests.py → pyGeno/tests/genome_tests.py

@@ -7,36 +7,21 @@
 
 class pyGenoSNPTests(unittest.TestCase):
 
-	def importAll(self) :
-		try :
-			importHumanReference_YOnly()
-		except ValueError :
-			pass
-			#~ print "--> Seems to already exist in db"
-
-		try :
-			importDummySRY()
-		except ValueError :
-			pass
-			#~ print "--> Seems to already exist in db"
-
-		self.ref = Genome(name = 'GRCh37.75_Y-Only')
-
 	def setUp(self):
-		self.importAll()
+		self.ref = Genome(name = 'GRCh37.75_Y-Only')
 
 	def tearDown(self):
 		pass
 
-	def testVanilla(self) :
+	def test_vanilla(self) :
 		dummy = Genome(name = 'GRCh37.75_Y-Only', SNPs = 'dummySRY')
 		persProt = dummy.get(Protein, id = 'ENSP00000438917')[0]
 		refProt = self.ref.get(Protein, id = 'ENSP00000438917')[0]
 
 		self.assertEqual('ATGCAATCATATGCTTCTGC', refProt.transcript.cDNA[:20])
 		self.assertEqual('HTGCAATCATATGCTTCTGC', persProt.transcript.cDNA[:20])
 
-	def testNoModif(self) :
+	def test_noModif(self) :
 		from pyGeno.SNPFiltering import SNPFilter
 
 		class MyFilter(SNPFilter) :
@@ -52,7 +37,7 @@ def filter(self, chromosome, dummySRY) :
 
 		self.assertEqual(persProt.transcript.cDNA[:20], refProt.transcript.cDNA[:20])
 
-	def testInsert(self) :
+	def test_insert(self) :
 		from pyGeno.SNPFiltering import SNPFilter
 
 		class MyFilter(SNPFilter) :
@@ -72,7 +57,7 @@ def filter(self, chromosome, dummySRY) :
 		self.assertEqual('ATGCAATCATATGCTTCTGC', refProt.transcript.cDNA[:20])
 		self.assertEqual('ATGATGCAATCATATGCTTC', persProt.transcript.cDNA[:20])
 
-	def testSNP(self) :
+	def test_SNP(self) :
 		from pyGeno.SNPFiltering import SNPFilter
 
 		class MyFilter(SNPFilter) :
@@ -90,7 +75,7 @@ def filter(self, chromosome, dummySRY) :
 		self.assertEqual('M', refProt.sequence[0])
 		self.assertEqual('L', persProt.sequence[0])
 
-	def testDeletion(self) :
+	def test_deletion(self) :
 		from pyGeno.SNPFiltering import SNPFilter
 
 		class MyFilter(SNPFilter) :
@@ -122,6 +107,16 @@ def test_find(self) :
 		self.assertEqual(len(prot)-10, prot.find(needle))
 
 def runTests() :
+	try :
+		importHumanReference_YOnly()
+	except ValueError :
+		print "--> Seems to already exist in db"
+
+	try :
+		importDummySRY()
+	except ValueError :
+		print "--> Seems to already exist in db"
+
 	unittest.main()
 
 if __name__ == "__main__" :

pyGeno/tools/parsers/CSVTools.py

@@ -70,6 +70,7 @@ def __init__(self, csvFile, lineNumber = None) :
 		self.data = []
 		if lineNumber != None :
 			self.lineNumber = lineNumber
+
 			tmpL = csvFile.lines[lineNumber].replace('\r', '\n').replace('\n', '')
 			tmpData = tmpL.split(csvFile.separator)
 
@@ -91,7 +92,11 @@ def __init__(self, csvFile, lineNumber = None) :
 
 	def __getitem__(self, key) :
 		"""Returns the value of field 'key'"""
-		return self.data[self.csvFile.legend[key.lower()]]
+		try :
+			indice = self.csvFile.legend[key.lower()]
+		except KeyError :
+			raise KeyError("CSV File has no column: '%s'" % key)
+		return self.data[indice]
 
 	def __setitem__(self, key, value) :
 		"""Sets the value of field 'key' to 'value' """
@@ -209,7 +214,7 @@ def next(self) :
 		self.currentPos += 1
 		if self.currentPos >= len(self) :
 			raise StopIteration
-		return CSVEntry(self, self[self.currentPos])
+		return CSVEntry(self, self.currentPos)
 
 	def __getitem__(self, line) :
 		if self.lines[line].__class__ is not CSVEntry :

setup.py

@@ -11,7 +11,7 @@
 setup(
     name='pyGeno',
 
-    version='1.1.6',
+    version='1.1.7',
 
     description='A python package for Personalized Proteogenomics',
     long_description=long_description,
@@ -21,7 +21,7 @@
     author='Tariq Daouda',
     author_email='[email protected]',
 
-	test_suite="pyGeno.tests.tests", 
+	test_suite="pyGeno.tests", 
 
     license='ApacheV2.0',