moved vector operations to their own library and can now calculate sc…

…ores for tissue specific expression

planet/models/expression_specificity.py

@@ -32,7 +32,7 @@ def calculate_specificities(species_id, description):
 
             print(profile_id, profile_mean)
             for condition in profile_data['order']:
-                expression_specificity(condition, profile_mean)
+                score = expression_specificity(condition, profile_mean)
 
 
 class ExpressionSpecificity(db.Model):

utils/expression.py

@@ -1,6 +1,15 @@
+from utils.vector import dot_prod, norm
+
 
 def expression_specificity(condition, profile):
     values = [v for k, v in profile.items()]
     vector = [v if k == condition else 0 for k, v in profile.items()]
 
-    print(values, vector)
+    dot_product = dot_prod(values, vector)
+
+    mul_len = norm(values) * norm(vector)
+
+    if mul_len != 0:
+        return dot_product/mul_len
+    else:
+        return 0

utils/vector.py

@@ -0,0 +1,21 @@
+from math import sqrt
+
+def dot_prod(a, b):
+    """
+    Calculates the dot product of two lists with values
+
+    :param a: first list
+    :param b: second list
+    :return: dot product (a . b)
+    """
+    return sum([i*j for (i, j) in zip(a, b)])
+
+
+def norm(a):
+    """
+    Calculates the Frobenius norm for a list of values
+
+    :param a: list of values
+    :return: the Frobenius norm
+    """
+    return sqrt(sum([abs(i)**2 for i in a]))