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/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',