Working with Files

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Working with Files

• HI5100 Data Structures for BioInformatics
• Lesson 6

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OBJECTIVES

• In this lesson you will learn
• About basic file processing and techniques for
  reading and writing text files.

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Lesson 6 Sections

• 1.1 File Processing
• Summary

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Files

• Many applications work with information that is
  stored in files external to the application
• There are different types of files
• We are going to focus on text files for now
• A file is information that is allocated to memory
  on a hard disk or other type of storage
• The file contains information that defines its
  own boundaries in memory

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Programs Using Files

• When an application is used to manipulate data in
  a file, the application has to contain code to
• Open the file
• So that info can be read from it
• Manipulate the file
• Read some or all of the information from the file
  into RAM
• Write info into the file in RAM
• Close the file
• Put an end of file (EOF) marker at the end of the
  file
• Save the file contents back to disk

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File Variables

• When a program is going to work with a file, a
  variable must be created that represents the file
  in the program

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Associate the File with a Variable
ltfilevargt open(ltpathgt,ltmodegt) NameFile
open(C\names.txt,r)

• ltmodegt is either
• r for read mode
• w for write mode

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Read from a File
ltfilevargt.read() ltfilevargt.readline() ltfilevargt.re
adlines()

• The read function reads the entire file into one
  (perhaps large) string
• The readline function reads the next line from
  the file as a string
• The readlines function reads the lines remaining
  in the file
• Newline characters separate one line from the next

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Create a Text File

• Use Microsoft Excel or a similar application to
  create a comma delimited text file (.csv) of,
  say, first names
• You can also create the file in Notepad
• Name the file names.csv

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A Program that Opens a File
open_and_print_file.py def main() fname
"names.csv" namelist open(fname,"r")
namedata namelist.read() print namedata

• Enter the program
• Save it in the same folder as names.csv
• Run it

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File Contents are Output
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Read Function

• The information was read from the file with Read
• Open names.csv in Notepad or Excel and rearrange
  the names so that there are more rows
• Save the changes and run the program in
  open_and_print_file.py again

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File Contents and Output
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Readline Function
open_and_print_file2.py def main() fname
"names.csv" namelist open(fname,"r")
for i_val in range(3) namedata
namelist.readline() print namedata

• Modify the program to use readline instead of
  read
• Save in the same folder as names.csv and run it

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Output Using Readline

• The program reads one line of the file at a time
• Then prints the line
• Stops after 3 lines. Why?
• What if the loop specifies more lines that there
  are in the file?

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Readlines Function

• Returns a list of lines
• Enables a program to iterate through the list

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Readlines Function
open_and_print_file3.py def main() fname
"names.csv" namelist open(fname,"r")
for line_val in namelist.readlines()
print line_val namelist.close()

• Modify the program to use readlines instead of
  readline
• Save in the same folder as names.csv and run it

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File and Output Using Readlines()
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You Can Loop Through Lines in the File Directly

• Without reading the file into RAM
• Here is the modified file

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Reading the File Directly Output
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Open a File for Writing

• If no file by the given name exists, a new file
  is created
• If a file with the given name does exist, it will
  be deleted and a new empty file is created
• Then the date is written into the new empty file

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Write to a File

• Open for writing
• Then use the write operation

ltfile-vargt.write(ltstringgt)
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Write Operation

• Takes a single value as an argument
• Argument must be a string
• Writes the string to a file
• If you want to start a new line in the file, you
  must explicitly provide a newline character
• \n is the newline character in Python (and in
  other languages)

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Write Data to a File
write_to_file1.py def main() namelist
open(namelist.dat,w) namelist.write(Daisy
Ducks nieces are named ) counter 1
namelist.write(April, ) counter counter
1 namelist.write(May, and ) counter
counter 1 namelist.write(June.\n)
namelist.write(Daisy Duck has d nieces.
counter) namelist.close()
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Output

• Where is the output?
• The output is a file named namelist.dat written
  to the same folder as the one containing the
  write_to_file1.py program
• Open the output file in Notepad

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Open Output File in Notepad
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Output File namelist.dat
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Summary

• Now you know a little about file handling in
  Python.
• You are ready for bigger and better things!

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End of Slides for Lesson 6

• HI5100 Data Structures for BioInformatics
• Lesson 6