Recursion

Genome 559: Introduction to Statistical and

Computational Genomics
Elhanan Borenstein
 A quick review

Returning multiple values from a function
return [sum, prod]

Pass-by-reference vs. pass-by-value

Python passes arguments by reference

Can be used (carefully) to edit arguments “in-place”

Default Arguments
def printMulti(text, n=3):

Keyword Arguments
runBlast(“my_fasta.txt”, matrix=“PAM40”)
 A quick review – cont’

Modules:

A module is a file containing a set of related functions

Python has numerous standard modules

It is easy to create and use your own modules:

Just put your functions in a separate file

To use a module, you first have

to import it:
import utils

Use the dot notation:

utils.makeDict()
So … what is a recursion and
what is it good for?
 Sorting algorithm

A sorting algorithm takes a list of elements in an
arbitrary order, and sort these elements in an
ascending order.

Commonly used algorithms:

Naïve sorting (a.k.a. selection sort)
Find the smallest element and move it to the
beginning of the list

Bubble sort
Swap two adjacent elements whenever they are not in
the right order

Merge sort
???
 The merge sort algorithm
1. Split your list into two halves

2. Sort the first half

3. Sort the second half

4. Merge the two sorted halves, maintaining a

sorted order
 Divide-and-conquer

The basic idea behind the merge sort algorithm is to
divide the original problem into two halves, each
being a smaller version of the original problem.

This approach is known as divide and conquer

Top-down technique

Divide the problem into independent smaller problems

Solve smaller problems

Combine smaller results into a larger result thereby
“conquering” the original problem.
 Merge sort – the nitty gritty
The merge sort algorithm That’s
simple
1
1. Split your list into two halves 2
2. Sort the first half ??? 3
1 5 3
3. Sort the second half Careful bookkeeping, 2 6 6
but still simple
4. Merge the two sorted halves, 5 8 10
8 10 20
maintaining a sorted order 12 12 28
21 20 31
21
28
If I knew how to sort, I wouldn’t be here in the 31
first place?!?
 Merge sort – the nitty gritty
The merge sort algorithm That’s
simple
1
1. Split your list into two halves 2
2. Sort the first half ??? 3
1 5 3
3. Sort the second half Careful bookkeeping, 2 6 6
but still simple
4. Merge the two sorted halves, 5 8 10
8 10 20
maintaining a sorted order 12 12 28
21 20 31
So … 21
how are we going to sort the two smaller lists? 28
31
Here’s a crazy idea: def mergeSort(list):

let’s use merge sort half1  first half of list

half2  second half of list
half1_sorted = mergeSort(half1)
half2_sorted = mergeSort(half2)

to do this list_sorted = merge(half1_sorted,half2_sorted)

return list_sorted
 You must be kidding, right?

WHAT? def mergeSort(list):
half1  first half of list
half2  second half of list
half1_sorted = mergeSort(half1)

This function has no loop? half2_sorted = mergeSort(half2)
list_sorted = merge(half1_sorted,half2_sorted)
return list_sorted

It seems to refer to itself!

Where is the actual sort?
this is making me dizzy!

What’s going on???
Let’s take a step back …
 Factorial

A simple function that calculates n!
# This function calculated n!
def factorial(n):
f = 1
for i in range(1,n+1):
f *= i
return f

>>> print factorial(5)

120
>>> print factorial(12)
479001600

This code is based on the standard definition of

factorial:
! = ∏ 
 Factorial

But … there is an alternative recursive definition:
 1 if n=0
n! = 
 ( n − 1)!× n if n>0

So … can we write a function that calculates n! using

this approach?
# This function calculated n!
def factorial(n):
if n==0:
return 1
else:
return n * factorial(n-1)

Well …
We can! It works! And it is called a recursive function!
 Why is it working?
# This function calculated n!
def factorial(n):
if n==0:
return 1
else:
return n * factorial(n-1)

factorial(5)
120
5 * factorial(4)
24
4 * factorial(3)
6
3 * factorial(2)
2
2 * factorial(1)
1
1 * factorial(0)
1
1
 Recursion and recursive functions

A function that calls itself, is said to be a recursive
function (and more generally, an algorithm that is defined in
terms of itself is said to use recursion or be recursive)

(A call to the function “recurs” within the function; hence the

term “recursion”)

In may real-life problems, recursion provides an

intuitive and natural way of thinking about a solution
and can often lead to very elegant algorithms.
 mmm…

If a recursive function calls itself in order to solve the
problem, isn’t it circular?
(in other words, why doesn’t this result in an infinite loop?)

Factorial, for example, is not circular because we

eventually get to 0!, whose definition does not rely on
the definition of another factorial and is simply 1.

This is called a base case for the recursion.

When the base case is encountered, we get a closed

expression that can be directly computed.
 Defining a recursion

Every recursive algorithm must have two key features:
1. There are one or more base cases for which no recursion
is applied.
2. All recursion chains eventually end up at one of the base
cases.

The simplest way for these two conditions

to occur is for each recursion to act on a
smaller version of the original problem.
A very small version of the original problem
that can be solved without recursion then
becomes the base case.
 This is fun!
Let’s try to solve (or at least think of)
other problems using recursion
 String reversal

Divide the string into first character and all the rest

Reverse the “rest” and append the first character to
the end of it
h e l l o w o r l d

reverse

d l r o w o l l e + h
See how simple and
elegant it is! No loops!

# This function reverses a string

def reverse(s):
return reverse(s[1:]) + s[0]

s[1:] returns all but the first character of the string. We reverse this
part (s[1:]) and then concatenate the first character (s[0]) to the end.
 String reversal - D’oh!
# This function reverses a string
def reverse(s):
return reverse(s[1:]) + s[0]

>>> print reverse(“hello world”)

Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "<stdin>", line 2, in reverse
File "<stdin>", line 2, in reverse
File "<stdin>", line 2, in reverse
File "<stdin>", line 2, in reverse
File "<stdin>", line 2, in reverse
File "<stdin>", line 2, in reverse
.
.
.
File "<stdin>", line 2, in reverse
File "<stdin>", line 2, in reverse
File "<stdin>", line 2, in reverse
File "<stdin>", line 2, in reverse
File "<stdin>", line 2, in reverse
RuntimeError: maximum recursion depth exceeded

What just happened? There are 1000 lines of errors!

 String reversal – Duh!

Remember: To build a correct recursive function, we
need a base case that doesn’t use recursion!
We forgot to include a base case, so our program is an infinite
recursion. Each call to “reverse” contains another call to
reverse, so none of them return.

Each time a function is called it takes some memory. Python

stops it at 1000 calls, the default “maximum recursion depth.”

What should we use for our base case?

 String reversal - Yeah

Since our algorithm is creating shorter and shorter
strings, it will eventually reach a stage when S is of
length 1 (one character).

Since a string of length 1 is its own reverse, we can
use it as the base case.
# This function reverses a string
def reverse(s):
if len(s) == 1:
return s
else:
return reverse(s[1:])+s[0]

>>> print reverse(“hello world”)

“dlrow olleh”
 Search a sorted list
(think phonebook)

How would you search a sorted list to check whether
a certain item appears in the list and where?

Random search (yep, I know, this is a stupid algorithm)

Serial search – O(n)

Binary search

hunting a lion in the desert

 Binary search
The binary-search algorithm
1. If your list is of size 0, return “not-found”.
2. Check the item located in the middle of your list.
3. If this item is equal to the item you are looking for:
you’re done! Return “found”.
4. If this item is bigger than the item you are looking for:
do a binary-search on the first half of the list.
5. If this item is smaller than the item you are looking for:
do a binary-search on the second half of the list.

How long does it take for this algorithm to find the query
item (or to determine it is not in the list)?
 Towers of Hanoi

There are three posts and 64 concentric disks shaped
like a pyramid.

The goal is to move the disks from post A to post B,
following these three rules:
1. You can move only one disk at a time.
2. A disk may not be “set aside”. It may only be stacked on
one of the three posts.
3. A larger disk may never be placed on top of a smaller one.
A B C
 Towers of Hanoi
Towers-of-Hanoi algorithm (for an “n disk tower”)
1. Move an “n-1 disk tower” from source-post to resting-post
(use the tower-of-hanoi algorithm)
2. Move 1 disk from source-post to destination-post
3. Move an “n-1 disk tower” from resting-post to destination-
post (use the tower-of-hanoi algorithm)

What should the base case be?

Assuming each disk move A B C
takes 1 second, how long
would it take to move
a 64 disk tower?
 Traversing a phylogenetic tree

Recursion is extremely useful when processing a data
structure that is recursive by nature.
def preorder(node):
if node == None:
return

print node.value, 10
preorder(node.left)
preorder(node.right)

preorder(root) 3 12
10 3 1 7 6 9 12 15

1 7 15

6 9
 Traversing a phylogenetic tree

Recursion is extremely useful when processing a data
structure that is recursive by nature.
def preorder(node):
if node == None:
return

print node.value, 10
preorder(node.left)
preorder(node.right)

preorder(root) 3 12
10 3 1 7 6 9 12 15

def postorder(node):
if node == None:
return
1 7 15
postorder(node.left)
postorder(node.right)
print node.value, 6 9
postorder(root)
1 6 9 7 3 15 12 10
 Finally,
let’s get back to our merge sort
The merge sort algorithm
1. Split your list into two halves
2. Sort the first half (using
merge sort)
3. Sort the second half (using
merge sort)
4. Merge the two sorted halves,
maintaining a sorted order
 # Merge two sorted lists
The merge sort algorithm def merge(list1, list2):
merged_list = []
1. Split your list into two halves i1 = 0
i2 = 0
2. Sort the first half (using

4 helper function
# Merge
merge sort) while i1 < len(list1) and i2 < len(list2):
if list1[i1] <= list2[i2]:
merged_list.append(list1[ii])
3. Sort the second half (using i1 += 1
merge sort) else:
merged_list.append(list2[i2])
i2 += 1
4. Merge the two sorted halves,
# One list is done, move what's left
maintaining a sorted order while i1 < len(list1):
merged_list.append(list1[i1])
i1 += 1
while i2 < len(list2):
merged_list.append(list2[i2])
i2 += 1

return merged_list

# merge sort recursive

def sort_r(list):
if len(list) > 1: # Still need to sort
half_point = len(list)/2
first_half = list[:half_point]
1 second_half = list[half_point:]

2 first_half_sorted = sort_r(first_half)
second_half_sorted = sort_r(second_half)
3
sorted_list = merge \
List of size 1. 4 (first_half_sorted, second_half_sorted)
Base case return sorted_list
else:
return list
 Recursion vs. Iteration

There are usually similarities between an iterative
solutions (e.g., looping) and a recursive solution.

In fact, anything that can be done with a loop can be done
with a simple recursive function!

In many cases, a recursive solution can be easily converted
into an iterative solution using a loop (but not always).

Recursion can be very costly!

Calling a function entails overhead

Overhead can be high when function calls are numerous
(stack overflow)
 Recursion vs. Iteration

Check the following two solutions for the Fibonacci
sequence:
# Returns the n-th Fibonacci number # Returns the n-th Fibonacci number
def fib_loop(n): def fib_rec(n):
prev = 0 if n == 1:
curr = 1 return 0
for i in range(n-2): elif n == 2:
curr, prev = curr+prev, curr return 1
return curr else:
return fib_rec(n-1)+fib_rec(n-2)

Which one would you prefer?

Recursion - the take home message

Recursion is a great tool to have in your problem-
solving toolbox.

In many cases, recursion provides a natural and
elegant solution to complex problems.

If the recursive version and the loop version are
similar, prefer the loop version to avoid overhead.

Yet, even in these cases, recursion offers a creative
way to think about how a problem could be solved.
 Sample problem #1

Write a function that calculates the sum of the
elements in a list using a recursion

Hint: your code should not include ANY for-loop or

while-loop!

Put your function in a module, import it into another

code file and use it to sum the elements of some list.
 Solution #1
utils.py
def sum_recursive(a_list):
if len(a_list) == 1:
return a_list[0]
else:
return a_list[0] + sum_recursive(a_list[1:])

my_prog.py
my_list = [1, 3, 5, 7, 9, 11]

from utils import sum_recursive

print sum_recursive(my_list)
 Sample problem #2

Write a recursive function that determines whether a
string is a palindrome. Again, make sure your code
does not include any loops.

A palindrome is a word or a sequence that can be read the

same way in either direction.

For example:

“detartrated”

“olson in oslo”

“step on no pets”
 Solution #2
def is_palindrome(word):
l = len(word)
if l <= 1:
return True
else:
return word[0] == word[l-1] and is_palindrome(word[1:l-1])

>>>is_palindrome("step on no pets")
True
>>>is_palindrome("step on no dogs")
False
>>>is_palindrome("12345678987654321")
True
>>>is_palindrome("1234")
False
 Challenge problems
1. Write a recursive function that prime factorize s an
integer number.
(The prime factors of an integer are the prime numbers that divide the
integer exactly, without leaving a remainder).
Your function should print the list of prime factors:
>>> prime_factorize(5624)
2 2 2 19 37
>>> prime_factorize(277147332)
2 2 3 3 3 3 3 7 7 11 23 23

Note: you can use a for loop to find a divisor of a number but the
factorization process itself should be recursive!

2. Improve your function so that it “returns” a list

containing the prime factors. Use pass-by-reference
to return the list.
3. Can you do it without using ANY loops whatsoever?
 Challenge solution 1
import math

def prime_factorize(number):

# find the first divisor

divisor = number
for i in range(2,int(math.sqrt(number))+1):
if number % i == 0:
divisor = i
break

print divisor,

if divisor == number: # number is prime. nothing more to do

return
else: # We found another divisor, continue
prime_factorize(number/divisor)

prime_factorize(277147332)
 Challenge solution 2
import math

def prime_factorize(number, factors=[]):

# find the first divisor

divisor = number
for i in range(2,int(math.sqrt(number))+1):
if number % i == 0:
divisor = i
break

factors.append(divisor)

if divisor == number: # number is prime. nothing more to do

return
else: # We found another divisor, continue
prime_factorize(number/divisor, factors)

factors = []
prime_factorize(277147332,factors)
print factors