1. File input and output
Genome 559: Introduction to Statistical and Computational Genomics
Prof. William Stafford Noble
Notes from 2009: Sample problem 4, the description differs from the example.
First “if-else” slide, must define seq.

2. <filehandle> = open(<filename>, <access type>)
Opening files
The open() command returns a file object.
<filehandle> = open(<filename>, <access type>)
Python can read, write or append to a file:
'r' = read
'w' = write
'a' = append
Create a file called “hello.txt” containing one line: “Hello, world!”
>>> my_file = open("hello.txt", "r")

3. Why is there a blank line here?
Reading the whole file
You can read the contents of the file into a single string.
>>> my_string = my_file.read()
>>> print my_string
Hello, world!
>>>
Why is there a blank line here?

4. Reading the whole file
Now add a second line to your file (“How ya doin’?”) and try again.
>>> my_file = open("hello.txt", "r")
>>> my_string = my_file.read()
>>> print my_string
Hello, world!
How ya doin'?
>>>

5. Reading the whole file
Alternatively, you can read the file into a list of strings.
>>> my_file = open("hello.txt", "r")
>>> my_string_list = my_file.readlines()
>>> print my_string_list
['Hello, world!\n', "How ya doin'?\n"]
>>> print my_string_list[1]
How ya doin'?

6. Reading one line at a time
The readlines() command puts all the lines into a list of strings.
The readline() command returns the next line.
>>> my_file = open("hello.txt", "r")
>>> my_string = my_file.readline()
>>> print my_string
Hello, world!
How ya doin'?
>>>

7. Writing to a file Open the file for writing or appending.
>>> my_file = open("new.txt", "w")
Use the <file>.write() method.
>>> my_file.write("This is a new file\n")
>>> my_file.close()
>>> ^D
> cat new.txt
This is a new file
Always close a file after you are finished reading from or writing to it.

8. Print vs write
<file>.write() does not automatically append an end-of-line character.
<file>.write() requires a string as input
>>> new_file.write("foo")
>>> new_file.write(1)
Traceback (most recent call last):
File "<stdin>", line 1, in ?
TypeError: argument 1 must be string or read-only character buffer, not int

9. <file> = open(<filename>, r|w|a)
<string> = <file>.read()
<string> = <file>.readline()
<string list> = <file>.readlines()
<file>.write(<string>)
<file>.close()

10. Sample problem #1
Write a program read-first-line.py that takes a file name from the command line, opens the file, reads the first line, and prints the result to the screen.
> python read-first-line.py hello.txt
Hello, world!
>

11. Solution #1 import sys filename = sys.argv[1]
my_file = open(filename, "r")
first_line = my_file.readline()
my_file.close()
print first_line

12. Sample problem #2
Modify your program to print the first line without an extra carriage return.
> python read-first-line.py hello.txt
Hello, world!
>

13. Solution #2 import sys filename = sys.argv[1]
my_file = open(filename, "r")
first_line = my_file.readline()
first_line = first_line[:-1]
my_file.close()
print first_line

14. Sample problem #3
Write a program add-two-numbers.py that reads one integer from the first line of one file and a second integer from the first line of a second file and then prints their sum.
> add-two-numbers.py nine.txt four.txt
9 + 4 = 13
>

15. Solution #3 import sys file_one = open(sys.argv[1], "r")
value_one = int(fileOne.readline())
file_two = open(sys.argv[2], "r")
value_two = int(fileTwo.readline())
print value_one, "+", value_two, "=", value_one + value_two

16. Sample problem #4 (optional)
sample.txt: 1 2 3 4 5
Write a program called print-nth-line.py that will extract a specified line from a given file.
python print-nth-line.py 2 sample.txt 2

17. Solution #4
import sys lineNumber = int(sys.argv[1]) file_name = sys.argv[2] infile = open(file_name, "r") lines = infile.readlines() print lines[lineNumber - 1]

18. Reading
Chapter 14 of Think Python (1st edition) by Allen B. Downey.