Transcript Slides - Edwards Lab

Advanced Python
Idioms
BCHB524
2014
Lecture 9
9/29/2014
BCHB524 - 2014 - Edwards
Outline

Sequences, iteration, and iterables

Comprehensions

Functional Programming

Exercises
9/29/2014
BCHB524 - 2014 - Edwards
2
Sequences and Iterables

Anything that supports:

Iterables we know about:





Strings, lists, sets, tuples
Dictionaries (keys(), values(), items())
Files (line by line)
Iterable → list, Iterable → set, etc.
Pair iterable → dictionary!
9/29/2014
BCHB524 - 2014 - Edwards
3
Iterables
# sequences are iterable -> build list
aList = list('abcdefabcdef')
print "String abcdefabcdef as a list:\n
",aList
# sequences are iterable -> build set (no duplicates)
aSet = set('abcdefabcdef')
print "String abcdefabcdef as a set:\n ",aSet
# Two iterables can be paired up using the zip function
keys = [1,2,3,4,5]
values = 'abcde'
aListOfPairs = zip(keys,values)
print "A list of pairs:\n ",aListOfPairs
# list of pairs are iterable -> build dict
aDict = dict(aListOfPairs)
print "A dictionary from a list of pairs\n
9/29/2014
BCHB524 - 2014 - Edwards
",aDict
4
Special Iterable Functions

zip


enumerate


single value from many
map, filter


iterates over (index of item, item)
sum, max, min, all, any


merges two or more iterables
Applies function or test to each element
sorted, reversed

9/29/2014
provides the items in sorted or reversed order
BCHB524 - 2014 - Edwards
5
Enumerate
# sequences are iterable -> build list
aList = list('abcdefabcdef')
# enumerate get index with item
for i,c in enumerate(aList):
print i,c
# exactly equivalent to
i = 0
for c in aList:
print i,c
i += 1
9/29/2014
BCHB524 - 2014 - Edwards
6
Map
# Numbers in a string... split into a list
numbers = '1,2,3,4,5,6'
number_list = numbers.split(',')
# Print the list, and manipulate its values!
print number_list
number_list[0] += 1
# Fix the problem, apply the int function to each item
number_list = map(int,number_list)
# Print the new list and check we can manipulate its values...
print number_list
number_list[0] += 1
print number_list
# Now to print it back out
print ",".join(number_list)
# Fix the problem, apply the str function to each item
number_list = map(str,number_list)
# Print the new list and check that we can do a join
print number_list
print ",".join(number_list)
9/29/2014
BCHB524 - 2014 - Edwards
7
Sorted, Reversed
# Make a list
aList = list('abcdefabcdef')
print "aList:\n ",aList
# print the list sorted and reversed...
print "Sorted:\n ",sorted(aList)
print "Reversed:\n ",reversed(aList)
print "Reversed in list:\n ",list(reversed(aList))
9/29/2014
BCHB524 - 2014 - Edwards
8
Comprehensions

Comprehensions build lists using iteration
[ expr for item in iterable ]
# Make the times two table..
timesTwo = [ 2*x for x in range(10) ]
# Make it another way
timesTwoToo = []
for x in range(10):
timesTwoToo.append(2*x)
print "timesTwo:\n ",timesTwo
print "timesTwoToo:\n ",timesTwoToo
9/29/2014
BCHB524 - 2014 - Edwards
9
Functional Programming

Python lets us treat functions as a basic
immutable data-type.
def f(x):
return 2*x
g = f
print f(1),g(2),f(3),g(4)

We can’t change them after they are defined,
but we can pass them in to functions.
9/29/2014
BCHB524 - 2014 - Edwards
10
sorted, revisited


The sorted function permits a keyword parameter: key
key is a function which returns the sort value
# Initialize a new list
aList = [1,-2,3,-4,5,-6]
# Print the list as is and sorted
print "aList:\n ",aList
print "Sorted:\n ",sorted(aList)
# Define absolute value sort key
def absSortKey(x):
return abs(x)
# Define negative value sort key
def negSortKey(x):
return -x
# Demonstrate alternative sorting keys
print "Sorted by absolute value:\n ",sorted(aList,key=absSortKey)
print "Sorted by negative value:\n ",sorted(aList,key=negSortKey)
9/29/2014
BCHB524 - 2014 - Edwards
11
Lambda functions


Sometimes, the functions are so simple, we don’t want to
define them formally.
 Usually used with sorted…
Useful key functions:
 Case insensitive:
sorted(words,key=lambda s: s.lower())

By dictionary value:
sorted(dict.items(),key=lambda p: p[1])

Also useful for map:
map(lambda x: 2*x, (1,2,3,4,5,6))
9/29/2014
BCHB524 - 2014 - Edwards
12
Exercises
Write a reverse complement function (and
package it up as a program) as compactly as
possible, using the techniques introduced
today.
1.
Hint: Use a dictionary for complement, map to apply
the get method, reversed, and join.

Write a program to compute and output the
frequency of each nucleotide in a DNA
sequence using a dictionary (see lec. 8).
2.

9/29/2014
Output the frequencies in most-occurrences to leastoccurrences order.
BCHB524 - 2014 - Edwards
13