Introduction to programming for Bioinformatics with Python

Python is a high-level programming language, that is, commands are described in a language close to the natural language. It is an interpreted language. Thus, Python depends on the Python interpreter for running scripts. It is also dynamic, strongly typed, object-oriented, and it has the peculiar characteristic of using code indenting to define the structure of blocks. So, while other programming languages use indenting only for code organization, in Python, indenting is vital for the correct functioning of scripts. Another striking feature of the language is the non-use of semicolons to terminate command lines.

Comments are pieces of code that will not be read by the interpreter, that is, comment regions will be ignored by the processor at execution time.

They are extremely important for code organization and documentation, that is, they serve to explain the function of a certain piece of code and to pass on different types of information, in case other programmers need to change your code or even you in the future.

Remember: good programmers always comment on their code.

The "if" statement performs conditional tests, and thus allows command blocks to be executed if a tested condition proves to be true.

Using the if statement, you can define which code blocks will be executed depending on different contexts and problems that your script tries to solve. We can understand then that conditional commands analyze whether a certain imposed condition is true or false, and allow different decisions to be made according to the validated data.

According to Python docs, "the while statement is used for repeated execution as long as an expression is true".

The "for" statement allows run a code block for each element of a list.

Hi. For some programming tasks, you will need to use data from external files or even record information after processing a script. In this class, you will learn how to work with files using Python.

To open a text file with Python, it is necessary to use the open function. The default syntax of the function is:

open(name, mode, buffering)

where “name” is the file that will be opened, “mode” is the way to open the file, and “buffering” is the number of bytes reserved in memory for opening the file (but mode and buffering are optional parameters). Additionally, this function can also be used to create new files. I will talk more about that later.

In programming, a function is a defined sequence of instructions or commands, which performs a specific task. Does this definition sound familiar? Hope so! So far, we have seen several built-in functions, such as print, open, or str.