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Numpy checklist: https://github.com/ageron/handson-ml/blob/master/tools_numpy.ipynb to come still: introduce sets as an iterable Cover topics mentioned here still: https://github.com/kgdunn/digital-skills-module5/blob/master/Notebooks/02.0%20NumPy%20arrays.ipynb

Consider elements from this notebook for module 1 and 2: https://nbviewer.jupyter.org/github/engineersCode/EngComp1_offtheground/blob/master/notebooks_en/2_Jupyter_strings_and_lists.ipynb

Containers

There are four collection data types in the Python programming language:

v List is a collection which is ordered and changeable. Allows duplicate members. v Tuple is a collection which is ordered and unchangeable. Allows duplicate members. v Dictionary is a collection which is unordered, changeable and indexed. No duplicate keys. TODO Set is a collection which is unordered and unindexed. No duplicate members.

Strings

  • M9: List comprehension. Find number of AGTC entries in a sequence.
  • M9: Read genome. Stop when you find first sequence of GATTAG

Lists

CAUTION! You cannot copy a list simply by typing species2 = species,

because: species2 will only be a reference to list1,

and changes made in species will automatically also be made in species2

species2 = species species2.append('wrong') Lists: cross reference: https://www.datacamp.com/community/tutorials/18-most-common-python-list-questions-learn-python

  • Copy by reference: show it by example

Count number od 'wrong' elements in the

'species list using the 'count' function

print("Number of wrong elements: {}".format(species.count('wrong')))

Make a list with first 10 elements of the

multiplication table of 2 (tafel van 2)

using "Python list comprehension"

print([2**x for x in range(1,11)])

if-else

M3: Go back to the quadratic example: solve for various values of a and b and c in the equation.

One-liner if statement: a = 3 b = 4 q = a if a < b else b

Example:

analysis_type = ['MACHINE_TTR', 'MACHINE_PH', 'CellCount method1', 'CellCount method2', 'CellCount method 3']

Write a one-liner if-else that returns a variable called axis_type which has the value of 'log' if the analysis_type contains the word 'CellCount', or otherwise returns the value 'linear'. Write a for loop that iterates over the analysis_type list, and returns the appropriate 'axis_type' value.

For loop

Newton's method with this plan (sketch out on paper)

  1. Initialize a
  2. Initialize x to a/2
  3. Repeat a few times:

Replace x by (x + a/x)/2 Display x

  1. Stop; show the true value

Vectorization: s = 0 for n = 1:100000 s += 1/n^**

Wait for numpy

n = arange(100000) s = sum( 1 / n**2 )

While loop

while True: print('Hi')

Infinite while loop. How to stop it?

While loop with += incremental operator; mention other operators are also possible: -= *= /=

Do while loop. Execute, then check: can be done with a break statement and condition check at end of a while True loop.

Example. Keep going until you see a particular DNA sequence. Or peak value above certain threshold

Types

change from one type to another:

  • float(45)
  • int(45.7)
  • round(45.7) # different result
  • chr(65)
  • Won't loose precision with ints. If a is int And multiplied by float, it is upgraded

Lists

Then you can iterate on that list, or do anything that lists can do. This section explores list methods

  • Find entries which appear more than once in a list
  • Common elements into two different lists. Join function equivalent?
  • Count how many entries in a list are greater than a threshold. List comprehension
  • Contrast with tuples. Seen before. Immutable concept introduced

NumPy

Try these elementwise operations on arrays yourself

  1. Calculating the absolute values: np.fabs(...) and np.absolute(...)
  2. Comparing two arrays and return the minimum np.fmin(...) and maximum np.fmax(...)
  3. The reciprocal value of $x$ is equal to $1/x$. You can calculate it using np.reciprocal(...)
  4. The sign of the values in the array: np.sign(...)

Exercises

  • 3D array: calculate summary values across each axis

Statistics part