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Workshop P1 (13th May 2021). Intro to programming and Python.

P1.1. Programming - basic concepts

  • Programming as a way of combining simple building blocks to achieve exactly what you need!
  • Diversity of programming languages, optimized for different tasks
  • Compiled vs interpreted programming languages
  • Python as a popular, powerful programming language with straightforward syntax and that we will use :)
  • Key challenge in programming is developing the way of thinking about the task, rather than about syntax!
     
  • I am not a formally trained bioinformatician. I do not know many sophisticated tools.
  • I learnt how to combine very simple tools into larger workflows effectively - and that has changed my research!
     

P1.2. Vocabulary (largely following Chapter 7!)

  • Program: A collection of instructions that can be executed by a computer to perform a specific task.
  • Script: A sequence of instructions that is interpreted or carried out by another program (interpreter).
  • Code: Noun: A program or a line of a program, sometimes called source code; Verb: The act of writing a program.
  • Execute/Run: To begin and carry out the operation of a program, or a portion of a program.
  • Variable: A component of a program, used to store information to be referenced and manipulated. Name matters!
  • Array: A data structure that contains a group of elements, used to organize data to facilitate sorting or searching.
  • Arguments: Values that are sent to a program at the time it is run.
  • Statement A line of a program or script which can assign a value, do a comparison, or perform another operation.
  • Function: A subprogram that can be called repeatedly to perform the same task within a program.
  • Parameters: Values that are sent to a function when it is called.
  • Return: The act of sending back a value by a function.
  • Parse: To extract particular data elements from a larger block of text.
     

P1.3. Variables

Each variable has several attributes. First attribute - the name, usually a p]ain word that gives some indication of the variable content. This needs to be informative!  

Second variable attiribute - "the type":

**Integer**                        0, 1, 2, 123456, -4321  
**Floating point (Float)**         0.12, 1.000, -123.56  
**Boolean**                        True, False == 1, 0  
**String**                        "Piotr", ">Seq123_456", "ACGTGTT", "123"

 

Third variable attiribute - "the value".
 

In some programming languages, you need to define the type when setting the variable. But Python 3 recognizes data type automatically, based on the value. Var1 = 0 Var2 = 1.234 Var3 = "ABC" Var4 = True  

You can check the variable type using the type() function:

type(Var1)
<class 'int'>
type(Var2)
<class 'str'>

 

You can also enforce the variable type:

Var4 = float(1)
Var5 = int(Var4)
Var6 = str(Var4)

 

Variables, or directly input objects can be used for various types of operations - as listed in a table 7.3 in Practical Computing for Biologists book:
Screenshot 2021-05-13 at 07 45 53  

P1.4. Arrays

Two primary types:

  1. List ---- of variables, or arrays! List of Lists!

  2. Dictionary {Key: Value} for example, {'Seq1': 'ACGT', 'Seq2': "ACCATG'} Dictionary of lists!  

Calling arrays in Python3:

List1 = []   # empty dictionary
NuclList = ['C', 'G', 'T', 'A']         # a list of nucleotides

NuclList                                # displays the list

type(List1) 
dir(List1)       # dir() function returns all properties and methods of the specified object

Objects in a list are numbered - each has an index position

NuclList[0]  # returns object with index no. 0 as a variable... remember they are indexed 0, 1, 2 ...
NuclList[1:]  # returns objects from the indicated position onwards, as a list!
&nbsp;  
  
List_of_seqs = [['Seq1', 'ACGTT'], ['Seq2', 'CCTTT']] # List of lists!
List_of_seqs[0][1]  # from list with index no. 0, return item with index no. 1
NuclList.append("N")

 

Note that string can be interpreted as a list of characters!

 

Dict1 = {}  
Dict2 = {'G': 'Guanine', 'C': 'Cytosine'}  
  
type(Dict2)
dir(Dict2)
  
Dict2['G']               # Extracting value correspondiong to key "G".
Dict2['A'] = 'Adenine'   # Adding a new key: value combination

 

P1.5. Flow control

Decisions with the if statement

if statement is the most widely used building block for decision making in the script - a sign at a fork in the road. if - elif - else construction will likely form an important part of your scripts!

if Value == 2:
    print("Couple")
elif Value in range(3,6):
    print("Few")
elif Value in range(6,10):
    print("Several")
else:
    print("Many")
Looping with for and while

The for loop iterates through a pre-defined list of objects:

for item in NucleotideList:
    print(item)

Sum = 0
for no in range(0,10):
    Sum += no
    print(no, Sum)

 

The while loop keeps iterating as long as the pre-defined condition is fulfilled:

Sum = 0
no = 0
while Sum < 100:
    Sum += no
    no += 1
    print(no, Sum)