Beginning Programming in Python

Fall 2019

Agenda

  • Files
    • Writing Files
    • Reading files
    • With keyword
    • For loops on file handles
    • Binary files
    • Large worked example (Fasta file processing)
    • Directories
    • Web file retrieval

source of input

  • User Input
    • Slow if needed to enter a lot of data
    • Error-prone: the user may enter wrong values
    • What if we want to run again?
    • What if we want an input based on inputs of previous executions.
  • Files
    • Enter data once into a file, save it, and reuse it.
    • Good for large amounts of data
    • Programs can use files to communicate
    • Need to be able to read from and write to files
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files

  • In Python, a file operation takes place in the following order:
    1. Open the file
    2. Read or write (perform operation)
    3. Close the file
  • Files can be opened for different purposes
    • Reading, writing, updating
  • Open files must be closed
    • To release the resources
    • To flush the output
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opening a file

  • To access a file, it must first be opened
  • The "open" function is used to open a file
    • <variable> = open(<path>, <mode>)
    • <variable> is of type file (file is a data type!)
    • <path> is the path and name of the file
    • <mode> is the opening mode (read, write, update)
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my_file = open("test.txt", "w")

opening modes

Mode Description
'r' Opens a file for reading (default)
'w' Opens a file for writing. Creates a new file if it does not exist
'a' Open for appending at the end of the file. Creates a new file if it does not exist.
'b' Opens in binary mode
'+' Opens a file for updating (reading & writing)

closing a file

  • When we are done with operations to the file, we need to properly close the file

  • The "close" method is used to close the file

 

 

 

  • It can be automatically done using "with" statement

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f = open('output.txt', 'w') 
# some operations here 
f.close()
with open("data.txt", "a+") as f:
	# some operations here
# now the file has been closed

writing to a file

Reading from a file

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  • When a file is opened for reading, an input pointer is positioned at the beginning of the file
  • After reading, the pointer is moved after the last read character
  • Reading in the text mode returns data in string
  • When the input pointer reaches the end of the file, any further read attempts results in an empty string

reading a file

"with" keyword

5 minutes break!

for loop on a file

Binary files

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  • Python can process binary files, which are just files with arbitrary bits in them
  • We can always treat a text file as a binary file, it's just that we ignore formatting
with open("test.txt", "rb") as f: # Here we treat test.txt as a binary file - any file
  # can be considered just a collection of bits
  with open("test2.txt", "wb") as g: # Note the nested with statements
    while True:
      buf = f.read(1024) # The argument to read tells it to read a set number of 
      # bytes - each byte is an 8 bit (8 0's or 1's) words into the "buf" object, 
      # which is a string
      if len(buf) == 0: # We're at the end
         break 
      g.write(buf)

directory Example

Downloading from web

Example

downloading data

Fasta file reading

Example

Fasta file example

Lecture 11 challenge

Questions?