File handling

BB1000 Programming in Python

KTH

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layout: false

Learning objectives

• File operations: open, close, read, write

• Handling of input and output with Python

• Usage of string, list

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The file system

Navigation

• The file system organizes data into files and directories (folders)

• Directories are special files that are contains of other files

• Often called a file tree

• The beginning of the tree is called the root “/”

• Directories are branches

• Files are leaves

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name: file-tree

A tree view of a file system

???

• Files names often have a dot, the latter part is the extension

• signifies type of file

• convention not requirement

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Where am I?

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name: looking

Looking around

Concept of location: current/working directory

$ pwd 
/home/jane
$ ls
file1  file1.bak  file1.tmp  tmp
$ ls /home/pablo
file1 file1.bak file2

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name: example

$ echo ~
/home/jane
$ echo ~pablo
/home/pablo
$ ls ../pablo
file1 file1.bak file2

Directory shortcuts

• ~ (home)

• . (current directory)

• .. (parent directory)

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name: moving

Moving around

• cd - change directory

$ cd ~pablo
$ pwd
/home/pablo
$ ls 
file1 file1.bak file2

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How do I view/change/save text in files?

--- name: files

Working with files and direcories

Files

Saving output in a file

• redirection (>)

• redirection with append (>>)

$ echo "Hello" >  /tmp/saved
$ ls  >>  /tmp/saved

What is in the file?

$ cat /tmp/saved
Hello
file1
file1.bak
file2

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name: edit

Edit a file with a text editor

$ nano /tmp/saved

  GNU nano 2.9.8                      /tmp/saved                                
____________________________________________________________________________

Hello
file1
file1.bak
file2












^G Get Help  ^O Write Out ^W Where Is  ^K Cut Text  ^J Justify   ^C Cur Pos
^X Exit      ^R Read File ^\ Replace   ^U Uncut Text^T To Spell  ^_ Go To Line

Remove the file

$ rm /tmp/saved

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name: directories

Directories

Creating and removing dictionaries

• mkdir create directory

• rmdir remove directory

$ mkdir thesis
$ cd thesis
$ nano thesis.tex
...

$ cd ..
$ rmdir thesis
rmdir: failed to remove 'thesis': Directory not empty
$ rm -r thesis

• be careful with this command!

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Opening files

The built-in open function

• open accepts a file name and a mode as arguments

• file name: a string

• mode: ‘r’ for reading; ‘w’ for writing

• open returns a file object

• after reading, the opened file should be closed

Getting help

Help on built-in function open in module io:                                     
                                                                                 
open(file, mode='r', buffering=-1, encoding=None, errors=None, newline=None, clos
efd=True, opener=None)                                                           
    Open file and return a stream.  Raise IOError upon failure.                  
                                                                                 
    file is either a text or byte string giving the name (and the path           
    if the file isn't in the current working directory) of the file to           
    be opened or an integer file descriptor of the file to be                    
    wrapped. (If a file descriptor is given, it is closed when the               
    returned I/O object is closed, unless closefd is set to False.)          

help(open)

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Reading/writing file

Methods of file objects:

• The read method Reads the entire file, unless a size argument is provided

• The readline method Reads one line from the file

• The readlines method Reads all lines from the file into a list

• The write method Accepts a string as argument, and writes the string to file

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Example: reading

Given a text file foo.txt

foo
bar
baz

>>> open('foo.txt').read()
foo
'foo\nbar\nbaz\n' 

>>> open('foo.txt').readlines()
['foo\n', 'bar\n', 'baz\n']          

>>> f = open('foo.txt')                                                          
>>> f.readline()                                                                 
'foo\n'                                                                          
>>> f.readline()                                                                 
'bar\n'                                                                          
>>> f.readline()                                                                 
'baz\n'                       

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File objects are iterables, which means you cat put them in a for loop. Text files are designed to return one line at at time

>>> for line in open('foo.txt'):
...     print(line)
foo

bar

baz

Why do we get an extra space?

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Example: writing

By default open expects an existing file for reading. To write to a file we need to give it a second parameter

>>> f = open('bar.txt', 'w')
>>> f.write('foo\n')
>>> f.write('bar\n')
>>> f.write('baz\n')
>>> f.close()

This will create a new file or overwrite an existing file

Note that you will not normally see any content in the file system until you have closed the file.

Alternative: you can supply the file object as an argument to print

f = open('bar.txt', 'w')
print('foo', file=f)
print('bar', file=f)
print('baz', file=f)
f.close()

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Closing files

It is good practice to close a file in the same program unit where opened

f = open('file.txt')
# work with file
# ...
f.close()

Howver, Python is very permissive about it so that if you forget, the file will close when you leave the function where it happened

Alternative way is to use a context manager (a with block)

with open('file.txt') as f:
    # work with file
    # ...

The file will be closed when you leave the with block

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Additional help:

https://docs.python.org/3/tutorial/inputoutput.html#reading-and-writing-files