class: title-slide, middle, center # Programming with Python (1) ## Robert Castelo [robert.castelo@upf.edu](mailto:robert.castelo@upf.edu) ### Dept. of Medicine and Life Sciences ### Universitat Pompeu Fabra <br> ## Fundamentals of Computational Biology ### BSc on Human Biology ### UPF School of Medicine and Life Sciences ### Academic Year 2024-2025 --- ## What's an algorithm * **Action**: an event that takes place in a finite period of time and produces an expected and well-defined result. -- * **Information**: anything we can observe or find out about an action. -- * **State**: the information available at a given time point. -- * **Algorithm**: sequence of actions starting at an initial state and ending at an end state, in which we obtain the result. -- [](img/gestiocasoscovid19.png) .footer[ [Gestió de casos COVID-19 als centres educatius](https://documents.espai.educacio.gencat.cat/IPCNormativa/Protocol-Gestio-casos-rev.pdf), Dept. de Salut, Generalitat de Catalunya, 9 de setembre de 2020. ] --- ## What's a software program * Building an algorithm consists of (1) discovering which elementary actions have to occur and (2) how they should be organised throughout time, to obtain the result. -- * Such an exercise requires: * Ability for **abstract thought** and **procedural abstraction** at different levels. * Using a language with precise syntax and notation. * Problem solving. * **Abstraction:** focus attention on the main problem, ignoring lower-level details. * **Procedural abstraction:** understand what a procedure should do without knowing exactly it how does it. -- * Writing a software program is **implementing** an algorithm in a specific programming language. --- ## Literals, constants and variables * [Literal](https://en.wikipedia.org/wiki/Literal_%28computer_programming%29): value that does not change over time, e.g.: <pre> 3.1416, 1, 2, 3, "Hello World!", ... </pre> * [Constant](https://en.wikipedia.org/wiki/Constant_%28computer_programming%29): named literal, a value that does not change over time but which we refer to it by a given name, typically written in upper case letters, e.g.: <pre> PI, A, B, C, ... </pre> * [Variable](https://en.wikipedia.org/wiki/Variable_%28computer_science%29): named container storing a value, which may change over time, e.g.: <pre> x, y, z, i, j, k, ... </pre> * Constant and variable names should consist of letters and/or digits, but they should not start with a digit. Underscores are allowed. E.g.: <pre> x1, y1, A4, result2, sum_of_squares, ... </pre> --- ## Assignments * [Assignment](https://en.wikipedia.org/wiki/Assignment_%28computer_science%29): statement that sets the value of a variable using an operator, `=` in Python, for instance: <pre> x = 1 x = 2 </pre> * In an assignment, the left-hand side of the assignment operator is always a variable, while the right-hand side is what we want to assign into the variable.  --- class: small-table ## Expressions * [Expression](https://en.wikipedia.org/wiki/Expression_%28computer_science%29): syntactically correct specification of one or more operations over any given set of literals, constants, variables or functions. E.g.: <pre> 1 + 1 x + 2 y / 2 </pre> * The right-hand side of an assignment can be an expression: <pre> x = x + 1 y = ( log(100) - x ) / 3 </pre> * Arithmetic operators | Operator | Example | Result | |--------------------- | :-------: | :-----: | | addition | 2 + 2 | 4 | | subtraction | 3 - 2 | 1 | | multiplication | 3 * 2 | 6 | | division (quotient) | 6 / 3 | 2 | | division (remainder) | 6 % 4 | 2 | --- ## Control flow * When we run an algorithm, there is a flow of actions being executed after one another. * The course of the flow of execution depends on the so-called [control flow](https://en.wikipedia.org/wiki/Control_flow) statements. * There are three main types of control flow statements: * Sequential: actions are executed in a particular order. * Conditional: one or more actions are executed only under a specific condition. * Iterative: one or more actions are executed multiple times until a specific condition is met. * In the next slides we will be using Python syntax to illustrate these control flow statements. --- class: small-table ## Control flow * Comparison operators: operators that compare two values and return a truth value, either `true` or `false`. | Description | Operator | |---------------------- | :-------: | | equality | == | | inequality | != | | greater than | > | | smaller than | < | | greater or equal than | >= | | smaller or equal than | <= | * `2 > 1` is `true`. * `2 < 1` is `false`. * `x > 0` will be `true` or `false` depending on the actual value of `x`. --- ## Control flow * Sequential control flow: <pre> a = 2 b = a b = b + a * 4 print(b) </pre> * The `print(b)` instruction will print the value of `b` in the terminal window. Think about what value is going to print in the previous code and in each of the two code blocks below. <pre> a = 2 b = a print(b) b = b + a * 4 </pre> <pre> a = 2 print(b) b = a b = b + a * 4 </pre> --- ## Control flow * Conditional control flow, also known as an "if statement": <pre> a = 4 b = 7 c = (a * b) + 1 if a % 2 == 0 :   print("even") else :   print("odd") </pre> * Code blocks associated with an `if` statement are defined by [whitespace](https://en.wikipedia.org/wiki/Whitespace_character) characters beginning each line of the associated code block. This is known in computer programming as [indentation](https://en.wikipedia.org/wiki/Indentation_style). Other programming languages (e.g., [C](https://en.wikipedia.org/wiki/C_%28programming_language%29), [Perl](https://en.wikipedia.org/wiki/Perl) or [JavaScript](https://en.wikipedia.org/wiki/JavaScript)) use curly braces, `{` and `}`, to define code blocks. * Programming languages, such as Python, which use indentation to define code blocks are said to adhere to the [off-side rule](https://en.wikipedia.org/wiki/Off-side_rule). --- ## Control flow * Conditional control flow, also known as an "if statement": <pre> a = 4 b = 7 c = (a * b) + 1 if a % 2 == 0 :   print("even") else :   print("odd") </pre> * What is going to print on the terminal window the previous Python code "even" or "odd"? --- ## Control flow * Iterative control flow, also known as a "while statement" or "loop": <pre> i = 0 s = 0 while i < 10 :   i = i + 1   s = s + i print(s) <pre> * What is it doing the previous code block with respect to the variable `s`? --- ## Problem solving * Problem: _"Write a program in Python that sums the first 10 natural numbers."_ -- _"Write a program in Python that calculates the incidence of COVID19."_ -- _"Write a program in Python that finds DNA mutations associated with cancer."_ -- .pull-left[ _"Write a program in Python that stiches together data collected from telescopes around the globe to produce an image of a black hole."_ .footer[ Image from an article in the New York Times in Spanish at https://www.nytimes.com/es/2019/04/15/espanol/katie-bouman-agujero-negro.html ] ] .pull-right[  ] --- ## Problem solving * Problem: _"Write a program in Python that sums the first 10 natural numbers."_ -- .pull-left[  ] .pull-right[  ] --  --- ## Problem solving * Problem: _"Write a program in Python that sums the first 10 natural numbers."_ .pull-left[  ] .pull-right[  ]  --- ## Problem solving * Problem: _"Write a program in Python that sums the first 10 natural numbers."_ .pull-left[  ] .pull-right[  ] -- * To figure out an algorithm, which you will end up writing it up as a program in Python, **you need first to come up with an schematic diagram**. --- ## Problem solving * Problem: _"Write a program in Python that sums the first 10 natural numbers."_ * Schematic diagram:  --- ## Problem solving * Implementation of the schematic diagram: <pre> i = 0 ## initial condition: should happen before looping s = 0 ## initial condition: should happen before looping while i < 10 : ## final condition: should not happen when looping   i = i + 1 ## invariant condition: always happens when looping   s = s + i   ## invariant condition: always happens when looping print(s) <pre> --- ## Concluding remarks * Spaces ([indentation](https://en.wikipedia.org/wiki/Indentation_style)) and newlines are important in Python to define control flow statements. -- * Syntax must be precise, otherwise we will encounter **syntax errors**. -- * Syntax errors are straightforward to correct, conceptual errors (when we do not obtain the right result) are much more difficult. We need to solve the problem correctly. -- * **Problem solving is key to learn programming**. -- * The right way to tackle a problem is to come up with an **schematic diagram** on paper, blackboard, etc. -- * There will be always a problem that is difficult enough for us that we will not be able to solve it correctly without an **schematic diagram**. -- * **The only way to learn problem solving is by solving problems**.