File input and output

and conditionals

Genome 559: Introduction to

Statistical and Computational Genomics
Prof. James H. Thomas
 Opening files
• The built-in open() command returns a file object:
<file_object> = open(<filename>, <access type>)

• Python will read, write or append to a file according

to the access type requested:
– 'r' = read
– 'w' = write (will replace the file if it exists)
– 'a' = append (appends to an existing file)

• For example, open for reading a file called "hello.txt":

>>> myFile = open('hello.txt', 'r')

 Reading the whole file
• You can read the entire content of the file
into a single string. If the file content is the
text “Hello, world!\n”:

>>> myString = myFile.read()

>>> print myString
Hello, world!

>>> why is there a

blank line here?
 Reading the whole file
• Now add a second line to the file (“How ya
doin’?\n”) and try again.

>>> myFile = open("hello.txt", "r")

>>> myString = myFile.read()
>>> print myString
Hello, world!
How ya doin'?

>>>
 Reading the whole file
• Alternatively, you can read the file into a list
of strings:

>>> myFile = open("hello.txt", "r")

>>> myStringList = myFile.readlines()
>>> print myStringList
['Hello, world!\n', 'How ya doin'?\n']
>>> print myStringList[1]
How ya doin'?
notice that each line this file method returns
has the newline a list of strings, one for
character at the end each line in the file
 Reading one line at a time
• The readlines() method puts all the lines into a list
of strings.
• The readline() method returns only the next line:

>>> myFile = open("hello.txt", "r")

>>> myString = myFile.readline()
>>> print myString
Hello, world! notice that readline()
automatically keeps track of
>>> myString = myFile.readline() where you are in the file - it
>>> print myString reads the next line after the
How ya doin'? one previously read

>>> print myString.strip() # strip the newline off

How ya doin'?
>>>
 Writing to a file
• Open a file for writing (or appending):
>>> myFile = open("new.txt", "w") # (or "a")

• Use the <file>.write() method:

>>> myFile.write("This is a new file\n")

>>> myFile.close()
>>> Ctl-D (exit the python interpreter)
> cat new.txt always close a file after
This is a new file you are finished reading
from or writing to it.

open("new.txt", "w") will overwrite an existing file (or create a new one)
open("new.txt", "a") will append to an existing file
 <file>.write() is a little
different from print()
• <file>.write() does not automatically
append a new-line character.
• <file>.write() requires a string as input.

>>> newFile.write("foo")
>>> newFile.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
>>> newFile.write(str(1)) # str converts to string

(also of course print() goes to the screen and <file>.write() goes to a file)
Conditional code execution
and code blocks

if-elif-else
 The if statement
>>> if (seq.startswith("C")):
... print "Starts with C"
...
Starts with C
>>>

• A block is a group of lines of code that belong together.

if (<test evaluates to true>):

<execute this block of code>

• In the Python interpreter, the ellipsis indicates that you are inside
a block (on my Win machine it is just a blank indentation).
• Python uses indentation to keep track of blocks.
• You can use any number of spaces to indicate a block, but you must
be consistent. Using one <tab> is simplest.
• An unindented or blank line indicates the end of a block.
 The if statement
• Try doing an if statement without indentation:

>>> if (seq.startswith("C")):
... print "Starts with C"
File "<stdin>", line 2
print "Starts with C"
^
IndentationError: expected an indented block
 Multiline blocks
• Try doing an if statement with multiple lines in the
block.

>>> if (seq.startswith("C")):
... print "Starts with C"
... print "All right by me!"
...
Starts with C
All right by me!

When the if statement is true, all of the lines in the

block are executed.
 Multiline blocks
• What happens if you don’t use the same number of
spaces to indent the block?

>>> if (seq.startswith("C")):
... print "Starts with C"
... print "All right by me!"
File "<stdin>", line 4
print "All right by me!"
^
SyntaxError: invalid syntax

This is why I prefer to use the <tab> character – it is always exactly correct.
Comparison operators used frequently
in conditional statements

• Boolean: and, or, not

• Numeric: < , > , ==, !=, >=, <=
• String: in, not in

< is less than

> is greater than
== is equal to
!= is NOT equal to
<= is less than or equal to
>= is greater than or equal to
 Examples
seq = 'CAGGT'
>>> if ('C' == seq[0]):
... print 'C is first'
... comparison
C is first operators
>>> if ('CA' in seq):
... print 'CA in', seq
...
CA in CAGGT
>>> if (('CA' in seq) and ('CG' in seq)):
... print "Both there!"
...
>>>
 Beware!
= versus ==

• Single equal assigns a value.

• Double equal tests for equality.

 Combining tests
x = 1
y = 2
z = 3
if ((x < y) and (y != z)):
do something
if ((x > y) or (y == z)):
do something else
Evaluation starts with the innermost parentheses and
works out. When there are multiple parentheses at the
same level, evaluation starts at the left and moves right.
The statements can be arbitrarily complex.

if (((x <= y) and (x < z)) or ((x == y) and not (x == z)))

 if-else statements
if <test1>:
<statement>
else:
<statement>

• The else block executes only if <test1> is false.

evaluates to
FALSE
>>> if (seq.startswith('T')):
... print 'T start'
... else:
... print 'starts with', seq[0]
...
starts with C
>>>
 if-elif-else
if <test1>:
<block1>
Can be read this way:
elif <test2>:
<block2> if test1 is true then run block1, else if
test2 is true run block2, else run block3
else:
<block3>

• elif block executes if <test1> is false and

then performs a second <test2>

• Only one of the blocks is executed.

 Example
>>> base = 'C'
>>> if (base == 'A'):
... print "adenine"
... elif (base == 'C'):
... print "cytosine"
... elif (base == 'G'):
... print "guanine"
... elif (base == 'T'):
... print "thymine"
... else:
... print "Invalid base!"
...
cytosine
<file> = open(<filename>, 'r'|'w'|'a')
<string> = <file>.read()
<string> = <file>.readline()
<string list> = <file>.readlines()
<file>.write(<string>)
<file>.close()

• Boolean: and, or, not if <test1>:

• Numeric: < , > , ==, <statement(s)>
!=, >=, <= elif <test2>:
• String: in, not in <statement(s)>
else:
<statement(s)>
 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!

>
 Solution #1
import sys
filename = sys.argv[1]
myFile = open(filename, "r")
firstLine = myFile.readline()
myFile.close()
print firstLine
 Sample problem #2
• Modify your program to print the first
line without an extra new line.

> python read-first-line.py hello.txt

Hello, world!
>
 Solution #2
import sys
filename = sys.argv[1]
myFile = open(filename, "r")
firstLine = myFile.readline()
firstLine = firstLine[:-1]
remove last character
myFile.close()
print firstLine
(or use firstLine.strip(), which removes all the whitespace from both ends)
 Sample problem #3
• Write a program math-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. If
the first number is smaller, then print their sum,
otherwise print their multiplication. Indicate the
entire operation in your output.

> add-two-numbers.py four.txt nine.txt

4 + 9 = 13
>
 Solution #3
import sys
fileOne = open(sys.argv[1], "r")
valOne = int(fileOne.readline()[:-1])
fileOne.close()
fileTwo = open(sys.argv[2], "r")
valTwo = int(fileTwo.readline()[:-1])
fileTwo.close()
if valOne < valTwo:
print valOne, "+", valTwo, "=", valOne + valTwo
else:
print valOne, "*", valTwo, "=", valOne * valTwo
Here's a version that is more robust because it doesn't matter
whether the file lines have white space or a newline:

import sys
fileOne = open(sys.argv[1], "r")
valOne = int(fileOne.readline().strip())
fileOne.close()
fileTwo = open(sys.argv[2], "r")
valTwo = int(fileTwo.readline().strip())
fileTwo.close()
if valOne < valTwo:
print valOne, "+", valTwo, "=", valOne + valTwo
else:
print valOne, "*", valTwo, "=", valOne * valTwo
 Sample problem #4 (review)
• Write a program find-base.py that takes as input a
DNA sequence and a nucleotide. The program should
print the number of times the nucleotide occurs in
the sequence, or a message saying it’s not there.

> python find-base.py A GTAGCTA

A occurs twice
> python find-base.py A GTGCT
A does not occur at all

Hint: S.find('G') returns -1 if it can't find the requested string.

 Solution #4
import sys
base = sys.argv[1]
sequence = sys.argv[2]
position = sequence.find(base)
if (position == -1):
print base, "does not occur at all"
else:
n = sequence.count(base)
print base, "occurs " + n + "times"
 Challenge problems
Write a program that reads a sequence file (seq1) and a sequence (seq2)
based on command line arguments and makes output to the screen that either:

1) says seq2 is entirely missing from seq1, or

2) counts the number of times seq2 appears in seq1, or
3) warns you that seq2 is longer than seq1

> python challenge.py seqfile.txt GATC

> GATC is absent
(or
> GATC is present 7 times)
(or
> GATC is longer than the sequence in seqfile.txt)
Make sure you can handle multiline sequence files.

Do the same thing but output a list of all the positions where seq2
appears in seq1 (tricky with your current knowledge).

TIP – file.read() includes the newline characters from a multiline file

 Challenge problems
Write a program that is approximately equivalent to the find and
replace function of word processors. Take as arguments: 1) a
string to find, 2) a string to replace with, 3) input file name, 4)
output file name. You don't really need this, but try to
incorporate a conditional test.

> f_and_r.py Watson Crick infile.txt outfile.txt

(should replace all appearances of "Watson" in the

input file with "Crick".)
 Reading

• First parts of chapters 5 and 14

from Think Python by Downey