1. Advanced Python Idioms
BCHB524 Lecture 9
BCHB524 - Edwards

2. Outline Sequences, iteration, and iterables Comprehensions
Functional Programming
Exercises
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3. 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!
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4. 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  ",aDict
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5. Special Iterable Functions
zip
merges two or more iterables
enumerate
iterates over (index of item, item)
sum, max, min, all, any
single value from many
map, filter
Applies function or test to each element
sorted, reversed
provides the items in sorted or reversed order
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6. 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
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7. 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)
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8. 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))
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9. 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
l1 = [ 2*x for x in range(10) ]
l2 = []
for x in range(10):
l2.append(2*x)
print l1
print l2
BCHB524 - Edwards

10. Functional Programming
Python lets us treat functions as a basic immutable data-type.
We can’t change them after they are defined, but we can pass them in to functions.
def f(x):     return 2*x g = f print f(1),g(2),f(3),g(4)
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11. 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)
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12. 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))
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13. Exercises
Write a reverse complement function (and package it up as a program) as compactly as possible, using the techniques introduced today.
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).
Output the frequencies in most-occurrences to least-occurrences order.
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14. Homework 5 Due Tuesday, October 9th. Submit using Canvas
Make sure you work through the exercises from the lecture.
Exercise 1 from Lecture 8
Exercises 1 and 2 from Lecture 9
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