add new implementaion of translation exercise

source/Dive_into_Functions.rst

@@ -151,7 +151,7 @@ help you by drawing diagram.
    .. image :: _static/figs/spacer.png   
     
 
-Exercice
+Exercise
 --------
 
 Without executing the code in Python interpreter, can you determine what the code below print out. 
@@ -181,7 +181,7 @@ help you by drawing diagram.
    .. image :: _static/figs/spacer.png   
     
     
-Exercice
+Exercise
 --------
 
 Without executing the code in Python interpreter, can you determine what the code below print out. 
@@ -211,7 +211,7 @@ help you by drawing diagram.
 
    .. image :: _static/figs/spacer.png   
        
-Exercice
+Exercise
 --------
 
 Without executing the code in Python interpreter, can you determine what the code below print out. 
@@ -240,7 +240,7 @@ help you by drawing diagram.
 
    .. image :: _static/figs/spacer.png   
     
-Exercice
+Exercise
 --------
 
 Without executing the code in Python interpreter, can you determine what the code below print out. 
@@ -276,7 +276,7 @@ help you by drawing diagram.
 
    .. image :: _static/figs/spacer.png   
     
-Exercice
+Exercise
 --------
 
 Without executing the code in Python interpreter, can you determine what the code below print out. 
@@ -307,7 +307,7 @@ help you by drawing diagram.
 
    .. image :: _static/figs/spacer.png   
     
-Exercice
+Exercise
 --------
 
 Without executing the code in Python interpreter, can you determine what the code below print out. 
@@ -336,7 +336,7 @@ help you by drawing diagram.
    .. image :: _static/figs/spacer.png   
     
     
-Exercice
+Exercise
 --------
 
 Without executing the code in Python interpreter, can you determine what the code below print out. 
@@ -375,7 +375,7 @@ help you by drawing diagram.
    .. image :: _static/figs/spacer.png   
     
     
-Exercice
+Exercise
 --------
 
 Without executing the code in Python interpreter, can you determine what the code below print out. 
@@ -410,7 +410,7 @@ help you by drawing diagram.
    .. image :: _static/figs/spacer.png   
     
       
-Exercice
+Exercise
 --------
 
 Without executing the code in Python interpreter, can you determine what the code below print out. 
@@ -474,14 +474,48 @@ bonus
 
 This function have to take the phase as parameter
 
+We will start to implement a function translating nucleic sequence only in phase 1
+
+first implementation:
+We will compute how many cycle we have to do and loop with a while
+
+.. literalinclude:: _static/code/translate.py
+   :linenos:
+   :lines: 4-50
+   :language: python
+
+second implementation:
+We will use a range to compute the stating position of each codon
+
+.. literalinclude:: _static/code/translate.py
+   :linenos:
+   :lines: 50-68
+   :language: python
+
+
+third implementation:
+We use a new function in the module itertools : `batched` that provide very nice feature for us.
+But this function is available **only** from `python 3.13`
+
 .. literalinclude:: _static/code/translate.py
    :linenos:
+   :lines:  1-4, 69-86
    :language: python
 
+
+Now we can implement the bonus (a translation with specifying the phase)
+
+.. literalinclude:: _static/code/translate.py
+   :linenos:
+   :lines:  87-
+   :language: python
+
+
 :download:`translate.py <_static/code/translate.py>` .
 
 
 .. _matrix_exercise:
+
 Exercise
 --------
 

source/_static/code/translate.py

+# this import is useful only for translate_3
+# and batched is available only from python3.13
+from itertools import batched
+
 genetic_code = { 'ttt': 'F', 'tct': 'S', 'tat': 'Y', 'tgt': 'C',
            'ttc': 'F', 'tcc': 'S', 'tac': 'Y', 'tgc': 'C',
            'tta': 'L', 'tca': 'S', 'taa': '*', 'tga': '*',
@@ -17,7 +21,9 @@ genetic_code = { 'ttt': 'F', 'tct': 'S', 'tat': 'Y', 'tgt': 'C',
       }
 
 def translate(nuc_seq, code):
-    
+    """
+    Trnaslate nuc_seq in phase 1 using the genetic code *code*
+    """
     prot_seq = ''
     n = 0
     # to avoid to compute len(seq)/3 at each loop
@@ -42,8 +48,57 @@ def translate(nuc_seq, code):
         # n += 3
     return prot_seq
 
-def translate2(nuc_seq, code, phase = 1):
+
+def translate_2(nuc_seq, code):
+    """
+    Translate nuc_seq in phase 1 using the genetic code *code*
+    """
+    prot_seq = ''
+    # we have to compute the position of the last codon
+    # otherwise if the seq length is not a multiple of 3
+    # we generate a codon with 2 or one base length
+    # and trigger an error when trying to translate it
+    for pos in range(0, len(nuc_seq) // 3 * 3, 3):
+        codon = nuc_seq[pos: pos + 3]
+        try:
+            prot_seq += code[codon]
+        except KeyError as err:
+            raise RuntimeError(f"Unknown codon: {codon}")
+    return prot_seq
+
+
+def translate_3(nuc_seq, code):
+    """
+    Translate nuc_seq in phase 1 using the genetic code *code*
+    """
+    # This implementation use a new function from the module itertools
+    # batched : https://docs.python.org/3/library/itertools.html#itertools.batched
+    # Warning batched is available from python 3.13 only
     prot_seq = ''
+    for codon in batched(nuc_seq, 3, strict=False):
+        if len(codon) < 3:
+            # it means that we are at the end of the sequence
+            # there is not enough bases to create a codon
+            break
+        else:
+            prot_seq += code[''.join(codon)]
+    return prot_seq
+
+
+def translate_with_phase(nuc_seq, code, phase = 1):
+    """
+    Translate the *nuc_seq* using the genetic code *code* in one of the 6 phases.
+
+    - phase 1: compute codons from the first base odf the sequence *nuc_seq*
+    - phase 2: compute codons from the second base
+    - phase 3: compute codons from the third base
+    - phase -1: compute codons from the first base but from the reversed sequence
+    - phase -2: compute codons from the second base but from the reversed sequence
+    - phase -3: compute codons from the third base but from the reversed sequence
+
+    :return: the aminoacid sequence
+    :rtype: str
+    """
     if 0 < phase < 4 :
         start = phase - 1
         nuc_seq = nuc_seq[start:]