avoid NaNs in the calculation of the mean score (David Arenillas, Uni…

…versity of British Columbia)

Bio/motifs/matrix.py

@@ -10,7 +10,7 @@
 from Bio.Seq import Seq
 from Bio.Alphabet import IUPAC
 
-#Hack for Python 2.5, isnan was new in Python 2.6
+#Hack for Python 2.5, isnan and isinf were new in Python 2.6
 try:
     from math import isnan as _isnan
 except ImportError:
@@ -19,6 +19,14 @@ def _isnan(value):
         if str(value).lower() == "nan":
             return True
         return value != value
+try:
+    from math import isinf as _isinf
+except ImportError:
+    def _isinf(value):
+        #This is tricky due to cross platform float differences
+        if str(value).lower().endswith("inf"):
+            return True
+        return False
 
 class GenericPositionMatrix(dict):
 
@@ -426,6 +434,8 @@ def mean(self, background=None):
                 logodds = self[letter,i]
                 if _isnan(logodds):
                     continue
+                if _isinf(logodds) and logodds < 0:
+                    continue
                 b = background[letter]
                 p = b * math.pow(2,logodds)
                 sx += p * logodds
@@ -448,6 +458,8 @@ def std(self, background=None):
                 logodds = self[letter,i]
                 if _isnan(logodds):
                     continue
+                if _isinf(logodds) and logodds < 0:
+                    continue
                 b = background[letter]
                 p = b * math.pow(2,logodds)
                 sx += p*logodds