In this example we have two ways to access to the list ``[1, 2]``.
If we modify the state of the list itself, but not the references to this object, then the two variables ``x`` and ``y`` still reference the list containing
``[1, 2, 3, 4]``.
Exercise
--------
wihout using python shell, what is the results of the following statements:
.. note::
sum is a function which return the sum of each elements of a list.
::
.. note::
``sum`` is a function that returns the sum of all the elements of a list.
Wihout using the Python shell, tell what are the effects of the following statements::
x = [1, 2, 3, 4]
x[3] = -4 # what is the value of x now ?
y = sum(x)/len(x) #what is the value of y ? why ?
y = 0.5
.. warning::
x[3] = -4 # What is the value of x now?
y = sum(x) / len(x) # What is the value of y? Why?
Solution (using the Python shell ;) )::
>>> x = [1, 2, 3, 4]
>>> x[3] = -4
>>> x
[1, 2, 3, -4]
>>> y = sum(x) / len(x)
>>> y
0.5
Here, we compute the mean of the values contained in the list ``x``, after having changed its last element to -4.
In python2 the result is ::
.. .. warning::
y = 0
..In python2 the result is ::
because sum(x) is an integer, len(x) is also an integer so in python2.x the result is an integer,
.. y = 0
.. because sum(x) is an integer, len(x) is also an integer so in python2.x the result is an integer,
all the digits after the periods are discarded.
Exercise
--------
Draw the representation in memory of the following expressions. ::
Draw the representation in memory of the ``x`` and ``y`` variables when the following code is executed::
x = [1, ['a','b','c'], 3, 4]
x = [1, ['a','b','c'], 3, 4]
y = x[1]
y[2] = 'z'
# what is the value of x?
# What is the value of x?
.. figure:: _static/figs/list_2-1.png
:width: 400px
:alt: set
:figclass: align-center
.. container:: clearer
.. image :: _static/figs/spacer.png
When we execute *y = x[1]*, we create ``y`` wich reference the list ``['a', 'b', 'c']``.
When we execute *y = x[1]*, we create ``y`` which references the list ``['a', 'b', 'c']``.
This list has 2 references on it: ``y`` and ``x[1]`` .
.. figure:: _static/figs/list_2-2.png
:width: 400px
:alt: set
:figclass: align-center
.. container:: clearer
.. image :: _static/figs/spacer.png
This object is a list so it is a mutable object.
So we can access **and** modify it by the two ways ``y`` or ``x[1]`` ::
x = [1, ['a','b','z'], 3, 4]
Exercise
--------
...
...
@@ -177,17 +188,23 @@ or ::
Exercise
--------
generate a list containing all codons.
.. note::
A codon is a triplet of nucleotides.
A nucleotide can be one of the four letters A, C, G, T
Write a function that returns a list containing strings representing all possible codons.
Write the pseudocode before proposing an implementation.
pseudocode:
"""""""""""
| *function all_codons()*
| *all_codons <- empty list*
| *let varying the first base*
| *for each first base let varying the second base*
| *for each combination first base, second base let varying the third base*
| *let vary the first base*
| *for each first base let vary the second base*
| *for each combination first base, second base let vary the third base*
| *add the concatenation base 1 base 2 base 3 to all_codons*
| *return all_codons*
...
...
@@ -201,14 +218,14 @@ first implementation:
python -i codons.py
>>> codons = all_codons()
:download:`codons.py <_static/code/codons.py>` .
:download:`codons.py <_static/code/codons.py>`.
second implementation:
""""""""""""""""""""""
Mathematically speaking the generation of all codons can be the cartesian product
between 3 vectors 'acgt'.
between 3 vectors 'acgt'.
In python there is a function to do that in ``itertools module``: `https://docs.python.org/3/library/itertools.html#itertools.product <product>`_
...
...
@@ -220,14 +237,14 @@ In python there is a function to do that in ``itertools module``: `https://docs.
>>> s = ">{name} {comment}\n{sequence}".format(id=id, comment=comment, sequence=sequence)
or
>>> s = f""{name} {comment} \n{sequence}"
>>> s = f">{name} {comment}\n{sequence}"
Exercise
--------
For the following exercise use the python file :download:`sv40 in fasta <_static/code/sv40_file.py>` which is a python file with the sequence of sv40 in fasta format
already embeded, and use python -i sv40_file.py to work.
