From f5609b5577496ef75d6634713c938a36d1327052 Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Mon, 21 Oct 2019 17:35:30 +0200
Subject: [PATCH] Add ReverseComplement function

---
 Code/ReverseComplement.py | 17 +++++++++++++++++
 Notebook.org              | 22 +++++++++++++---------
 2 files changed, 30 insertions(+), 9 deletions(-)
 create mode 100644 Code/ReverseComplement.py

diff --git a/Code/ReverseComplement.py b/Code/ReverseComplement.py
new file mode 100644
index 0000000..de6b4ef
--- /dev/null
+++ b/Code/ReverseComplement.py
@@ -0,0 +1,17 @@
+def ReverseComplement(Pattern):
+    Pattern = Reverse(Pattern)
+    Pattern = Complement(Pattern)
+    return Pattern
+
+
+def Reverse(Pattern):
+    reversed = Pattern[::-1]
+    return reversed
+
+
+def Complement(Pattern):
+    compl = ""
+    complement_letters = {"A": "T", "T": "A", "C": "G", "G": "C"}
+    for char in Pattern:
+        compl += complement_letters[char]
+    return compl
diff --git a/Notebook.org b/Notebook.org
index 81ffd9b..272959e 100644
--- a/Notebook.org
+++ b/Notebook.org
@@ -8,17 +8,21 @@
     
      Locating an ori is key for gene therapy (e.g. viral vectors), to introduce a theraupetic gene.
      
-**** Exercise: computational approach to find ori in bacteria
+**** Exercises: computational approaches to find ori in Vibrio Cholerae
      
-     We'll look for the *DnaA box* sequence, using a sliding window, in that case our code would be the following:
+***** Exercise: find Pattern
+     
+     We'll look for the *DnaA box* sequence, using a sliding window, in that case we will use the function [[./Code/Replication.py][Replication]] to find out how many times
+     does a sequence appear in the genome.
+     
+     For the second part, we're going to calculate the frequency map of the sequences of length /k/, for that purpose we'll use [[./Code/FrequentWords.py][FrequentWords]] 
+     
+***** Exercise: Find the reverse complement of a sequence
+     
+      We're going to generate the reverse complement of a sequence, which is the complement of a sequence, read in the same direction (5' -> 3').
+      In this case, we're going to use [[./Code/ReverseComplement.py][ReverseComplement]] 
+      After using our function on the Vibrio's Cholerae genome, we realize that some of the frequent k-mers are reverse complements of other frequent ones.
      
-    #+begin_src python
-      count = 0
-      
for i in range(len(Text)-len(Pattern)+1):
-        if Text[i:i+len(Pattern)] == Pattern:
-          count = count+1 
-      print(Pattern + ": " + count)
-    #+end_src 
 
 *** Vocabulary
       - k-mer: subsquences of length /k/ in a biological sequence