From e25a21fb861de80b46a8a6c513eeaabc4303ef05 Mon Sep 17 00:00:00 2001
From: sepro <sebastian.proost@gmail.com>
Date: Tue, 22 Mar 2016 15:41:53 +0100
Subject: [PATCH] moved vector operations to their own library and can now
 calculate scores for tissue specific expression

---
 planet/models/expression_specificity.py |  2 +-
 utils/expression.py                     | 11 ++++++++++-
 utils/vector.py                         | 21 +++++++++++++++++++++
 3 files changed, 32 insertions(+), 2 deletions(-)
 create mode 100644 utils/vector.py

diff --git a/planet/models/expression_specificity.py b/planet/models/expression_specificity.py
index 883a3ad..0f89023 100644
--- a/planet/models/expression_specificity.py
+++ b/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):
diff --git a/utils/expression.py b/utils/expression.py
index b38d38b..5dacd9f 100644
--- a/utils/expression.py
+++ b/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)
\ No newline at end of file
+    dot_product = dot_prod(values, vector)
+
+    mul_len = norm(values) * norm(vector)
+
+    if mul_len != 0:
+        return dot_product/mul_len
+    else:
+        return 0
diff --git a/utils/vector.py b/utils/vector.py
new file mode 100644
index 0000000..f299621
--- /dev/null
+++ b/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]))
\ No newline at end of file