Programming with Python and Biopython: Glossary

Python programs are plain text files.

Use the Jupyter Notebook for editing and running Python.

The Notebook has Control and Edit modes.

Use the keyboard and mouse to select and edit cells.

The Notebook will turn Markdown into pretty-printed documentation.

Markdown does most of what HTML does.

Use variables to store values.

Use print to display values.

Variables persist between cells.

Variables must be created before they are used.

Python is case-sensitive.

Use meaningful variable names.

Variables can be used in calculations.

Every value has a type.

Use the built-in function type to find the type of a value.

Types control what operations can be done on values.

Strings can be added and multiplied.

Strings have a length (but numbers don’t).

Must convert numbers to strings or vice versa when operating on them.

Can mix integers and floats freely in operations.

Variables only change value when something is assigned to them.

A function may take zero or more arguments.

Commonly-used built-in functions include max, min, and round.

Functions may only work for certain (combinations of) arguments.

Functions may have default values for some arguments.

Use the built-in function help to get help for a function.

The Jupyter Notebook has two ways to get help.

Every function returns something.

Use comments to add documentation to programs.

Python reports a syntax error when it can’t understand the source of a program.

Indentation is meaningful in Python.

Python reports a runtime error when something goes wrong while a program is executing.

Fix syntax errors by reading the source code, and runtime errors by tracing the program’s execution.

Most of the power of a programming language is in its libraries.

A program must import a library in order to use it.

Use help to find out more about a library’s contents.

Import specific items from a library to shorten programs.

Create an alias for a library when importing it to shorten programs.

A list stores many values in a single structure.

Use an item’s index to fetch it from a list.

Lists’ values can be replaced by assigning to them.

Appending items to a list lengthens it.

Use del to remove items from a list entirely.

The empty list contains no values.

Lists may contain values of different types.

Character strings can be indexed like lists.

Character strings are immutable.

Indexing beyond the end of the collection is an error.

A for loop executes commands once for each value in a collection.

The first line of the for loop must end with a colon, and the body must be indented.

A for loop is made up of a collection, a loop variable, and a body.

Loop variables can be called anything (but it is strongly advised to have a meaningful name to the looping variable).

The body of a loop can contain many statements.

Use range to iterate over a sequence of numbers.

The Accumulator pattern turns many values into one.

Use if statements to control whether or not a block of code is executed.

Conditionals are often used inside loops.

Use else to execute a block of code when an if condition is not true.

Use elif to specify additional tests.

Conditions are tested once, in order.

Create a table showing updates to variables’ values to trace the execution of a program.

A set stores unsorted unique values.

The set list contains no values.

Sets may contain values of different types.

Install and load Biopython

Use Biopython to load sequence files

Work with sequence records

Convert formats

Write new records with your own content

Break programs down into functions to make them easier to understand.

Define a function using def with a name, parameters, and a block of code.

Defining a function does not run it.

Arguments in call are matched to parameters in definition.

Functions may return a result to their caller using return.

Follow standard Python style in your code.

Use docstrings to provide online help.

Know what code is supposed to do before trying to debug it.

Make it fail every time.

Make it fail fast.

Change one thing at a time, and for a reason.

Keep track of what you’ve done.

Be humble.

Fail early, fail loudly.

Can use if, print, and sys.exit to detect and report errors.

Use assert to check internal correctness.

Practice defensive programming.

Practice test-driven development.

Use the Pandas library to do statistics on tabular data.

Use index_col to specify that a column’s values should be used as row headings.

Use DataFrame.info to find out more about a data frame.

The DataFrame.columns variable stores information about the data frame’s columns.

Use DataFrame.T to transpose a data frame.

Use DataFrame.describe to get summary statistics about data.

Use DataFrame.ix[..., ...] to select values by location.

Use : on its own to mean all columns or all rows.

Select multiple columns or rows using DataFrame.ix and a named slice.

Result of slicing can be used in further operations.

Use comparisons to select data based on value.

Select values or NaN using a Boolean mask.

Python supports a large community within and outwith research.

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