11 – File I/O

COMP 125 – Programming with Python

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File I/O Basics
How can we save data for later use?
▪ Word processors: write letters, reports, etc.
▪ Image editors: draw graphics and edit images
▪ Spreadsheets: insert numbers and mathematical formulas
▪ Games: list of player names, scores, current game status
▪ Web browsers: contents of shopping carts, etc.

You will learn:

▪ How to open a file
▪ How to read from a file
▪ How to write into a file
▪ How to close a file

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Filenames and file objects
▪ Files are identified by a filename
▪ Examples: [Link] , [Link] ,
[Link]

▪ Filename extensions represent the

type of data stored
▪ Examples: .jpg, .txt , .docx, .py

▪ The program must create a file

object in memory to work with a file
on the computer’s disk

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Opening a file
name of the variable
referencing the file object
string specifying the
name of the file

Mode in which the file will

be opened (reading, writing, etc.)

Some of the file open modes:

Method Description
‘r' Open a file for reading only. The file cannot be changed or written to.

‘w’ Open a file for writing. If the file already exists, erase its contents. If it doesn ot exist, create it.

‘a’ Open a file to be written to. All data written to the file will be appended to its end. If the file does not exist, create it.

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Closing a file
▪ Do not forget to close the file once you are done
▪ close() disconnects the program from the file to prevent data loss

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File locations - paths

▪ Files are kept on the secondary storage using file systems

▪ Almost all common file systems organize files into hierarchies (which form a
tree) using drives and folders

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File locations - paths

▪ When opening files, you can specify an absolute path or a relative path
▪ Relative path is relative to the “current working directory (cwd)”
▪ To learn the current working directory:

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File locations - paths

▪ When file is in the same folder as the Python program (or nearby), using
relative paths makes things easy:

▪ Examples with absolute paths:

▪ Mac:
▪ Windows:

Specifies that the string is a raw string

(backlash characters are read as literal backslashes)

▪ If you need to, you should use relative paths in the homework (why?)
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Writing data into a file

It accepts a single string

as an argument

Don’t forget to close the file

once you are done!
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Example
▪ Grocery list: write each item and it’s quantity on a separate line in a file.

items = ["bread", "butter", "eggs", "milk", "pasta"]

quantity = [2, 1, 12, 3, 2]

fvar = open("grocery_list.txt", "w")

for i in range(len(items)):
[Link](items[i]+"\t"+str(quantity[i])+"\n")
[Link]()

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Example
▪ Add 5 bananas at the end of the file that you created in the previous
example.

fvar = open("grocery_list.txt", "a")

[Link]("banana"+"\t"+str(5)+"\n")
[Link]()

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Reading data from a file

▪ Open your file for reading (with ‘r’ method)

▪ Use the readline method to read one line at a time
▪ readline: File object function that reads a line from the file
▪ Line returned as a string, including ‘\n’

Alternatives
▪ read: File object function that reads entire file contents into memory
▪ Contents returned as a string
▪ readlines: File object function that reads entire file contents
▪ Contents returned as a list of lines where each line is a string including ‘\n’

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Using readline
▪ Reads the file contents, one line at a time

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Example
▪ Suppose that you have the following file that
contains the department abbreviations and the
course codes separated with white space.

readline returns empty string

when End of File is reached

▪ Write a function that takes the name of this file

as its input, reads its contents, and returns a list
of course tuples. You may assume that the file
content is always valid.

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Using a for loop

▪ for loop automatically reads the lines in a file

▪ without requiring a priming read operation
▪ without testing a special condition that signals the end of the file

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Example (using for)

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Alternative way to open a file: ’with’ statement

[Link]() is not required

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Common errors

▪ What happens if your input file does not exist?

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Common errors

▪ What happens if the path of your output file does not exist?

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How to handle exceptions
▪ Try/Except body captures the error and lets you decide how to handle it.

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File I/O with String Formatting
Some useful functions to process strings

rstrip(): returns a copy of the string with all

trailing whitespace characters are removed (at
the end, i.e., Right side)
▪ Useful to get rid of the newline character

lstrip(): returns a copy of the string with all

leading whitespace characters are removed
(at the beginning, i.e., Left side)

strip(): returns a copy of the string with all

leading and trailing whitespace characters are
removed

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Reading and writing numeric data

Now you can perform

math operations

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Example
▪ Write a function that creates an output
file with name number_list.txt and writes
the numbers 1 through 100 to that file.

▪ Write a function that opens the

number_list.txt file you created, reads
the numbers from the file, and displays
them.

▪ Write a function that adds all numbers it

read from the number_list.txt file and
displays their total.

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Example
▪ Suppose that you have the following file that contains the exam grades of students

▪ Write two functions:

▪ The first function takes the name of this file as its input, reads its contents, and returns a list of student tuples. The fi rst
item in each tuple is the student id as a string and the second item is a list of three integer grades. You may assume
that the file always contains valid content.
▪ The second function takes the list of student tuples together with an output file name as its inputs. For each student, it
calculates the average of the grades and saves these averages in the output file together with the students’ IDs.

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Solution

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CSV Files
Working with CSV files
▪ CSV file = “comma separated values” file
▪ Each line of the file is a data record
▪ Each record consists of one or more fields, separated by commas

▪ How to edit CSV files?

▪ Spreadsheet Apps
▪ MS Excel, Apple Numbers,
Google Sheets, OpenOffice or
LibreOffice
▪ Text Editing Apps
▪ WordPad, TextEdit, Vim, Emacs,
etc.
▪ Programming Editor Apps
▪ Spyder, PyCharm, VS Code, etc.

CSV = comma-separated values

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CSV files

Spreadsheet view: Text editor view:

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Writing data into a .csv file
▪ Writing into the same column

If not string, use

str to convert to a
string
▪ Writing into the same row

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Reading data from a .csv file
▪ Reading the items from a column

▪ Reading the items from a row

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Example
▪ Proteins are composed of 20 different types
of amino acids.
▪ The sequence of a protein can be shown by
using the single letter representation for each
amino acid. (e.g. Glycine: G)

▪ Ubiquitin amino acid sequence:

“MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDK
EGIPPDQQRLIFAGKQLEDGRTLSDYNIQKES
TLHLVLRLRGG”

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Example atomid atom name
x, y, z coordinates
▪ The file [Link]
contains atom information
for the protein 1ubq
▪ From the lines starting
with ATOM keyword, copy
the following to a new csv
file:
▪ atomid
▪ atom name
▪ x, y, z coordinates

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Solution

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