CSE 111 Bio: Program Design I Lecture 5: More Strings, Intro Lists, Translation & Central Dogma of Biology

Transcription

1 CSE 111 Bio: Program Design I Lecture 5: More Strings, Intro Lists, Translation & Central Dogma of Biology Robert Sloan (CS) & Rachel Poretsky (Bio) University of Illinois, Chicago September 12, 2017

2 What does this code print? x = "Go" y = "Flames!" print(x + y) A. Go Flames! B. GoFlames! C. Error because the addition is illegal D. Go

3 Admin: Midterm 1 no sooner than 9/28 Midterm 1 moved. Thursday 9/28 (slightly tentative, could be a little later) We really don't want to schedule any hour exam on a day when a student will be out for a religious holiday so we did that Piazza poll

4 Review: Indexing strings [i] after string gives character number i Important: Python (and many computer scientists!) counts from 0, not from 1! A A T G C C G T G C T T After: my_dna = "AATGCCGTGCTT" my_dna[2] à 'T'

5 Negative indices Sometimes we want to get our hands on the last character of a string One way: my_dna[len(my_dna) 1] Why is that 1 in there? Because my_dna string has 11 characters, so length 11, but characters numbered 0, 1, 2,, 10 and in general the characters of string s are numbered 0, 1,, len(s) 1

6 Negative indices Sometimes we want to get our hands on the last character of a string One way: my_dna[len(my_dna) 1] Another, often easier to think about way: Index 1 is always last character of string And index -2 2 nd last character, and so on So my_dna[-1] à 'T'; my_dna[-3] à 'C' A A T G C C G T G C T T

7 Slicing: Getting part of a string Substring of a string is called slice s[m:n] returns characters from index m (counting from 0 as always) up to but not including character n bt = "Dr. Rosalind Franklin" bt[0:3] à 'Dr.' bt[4:12] à 'Rosalind'

8 Slicing: omission = start/end bt = "Dr. Rosalind Franklin" bt[:12] à 'Dr. Rosalind' bt[13:] à 'Franklin' and sort of silly one: bt[:] à 'Dr. Rosalind Franklin'

9 Trivia: Over end treated as end >>> s = "Register to vote!" In [1]: s[9:11] Out[1]: 'to' In [2]: s[12:20] Out[2]: 'vote!'

10 Using strings: slicing (Recap & check) >>> mydna = "AATGCCGTGCTT" >>> mydna[0:4] 'AATG' >>> mydna[3:7] 'GCCG >>> mydna[1:] 'ATGCCGTGCTT' >>> mydna[:4] 'AATG' A A T G C C G T G C T T TGCTT? A. mydna[5] B. mydna[7:11] C. mydna[7:12] D. mydna[7:len(mydna)] E. No clue

11 Fancy slicing you'll almost never use You are allowed to give 3 indices, which are interpreted as start:end:step bt = "Dr. Rosalind Franklin" bt[4:17:3] à RanFn'

12 Strings: lots of other thing too! (Lab hint!) Strings have many built-into-python methods for doing lots of useful things. Will cover in detail in next few weeks. One example for now: Counting occurrence of letter (or any substring in a string): with the.count() string method: sentence = 'Mary had a little lamb' sentence.count('a') à 4 sentence.count('had') à 1 sentence.count('t') à 0

13 Some people objects just never change In Python, integers are immutable Cannot assign to integer object I.e., cannot write 1 = 0 Probably not a surprise Important: strings are immutable too! first_codon = "ACT" first_codon[0] = "G" Illegal; ERROR!

14 But Professor Can write n = 1 n = 0 Is that changing an integer?

15 But Professor Can write n = 1 n = 0 Is that changing an integer? NO! Changing which object variable name n is assigned to Could reassign (entire object of) first_codon too

16 Pictures Some immutable objects in memory n first_codon 1 'ACT'

17 Pictures Some immutable objects in memory n first_codon 0 1 'ACT' n = 0 doesn't change immutable integer 1, just the assignment of a variable to an object

18 Pictures Some immutable objects in memory n first_codon 0 1 'ACT' first_codon = 0 doesn't change immutable integer 1, just the assignment of a variable to an object

19 Problem with first_codon[0] = 'G' Some immutable objects in memory first_codon 'ACT' first_codon[0] = "G" illegal because cannot change contents of any blue boxes. Those objects are immutable

20 Coming attractions: Mutable types Numbers, Booleans, and strings are all immutable Python does have some mutable types Two very important ones we will see are Lists and dictionaries

21 Lists: Brief Overview Slower with more details coming

22 Lists >>> primes = [2,3,5,7,11] >>> biologists = ["james","francis","rosalind"] >>> L = [2, zebra", 11] >>> M = [2, zebra", 11, ["spam","spamity","spam"] ]

23 Lists index/slice the same as strings >>> M = [2, zebra", 11, ["spam","spamity","spam"] ] >>> len(m) 4 >>> M[2] 11 >>> M[3] ['spam', 'spamity', 'spam'] >>> M[3][0] A. ["spam","spamity","spam"], B. ['spam'] C. 'spam' D. Error E. No clue >>> M[2:] A. 11 B.[11] D.[11, ["spam","spamity","spam"]] E. [11, "spam","spamity","spam"]

24 Addition in lists >>> my_list = [42, 47, 23] >>> newlist = my_list BARF! >>> newlist = my_list + [100] >>> newlist [42, 47, 23, 100] >>> my_list [42, 47, 23] >>> newlist = newlist + newlist >>> newlist A. [42, 47, 23, 100, 42, 47, 23, 100] B. [42, 47, 23, 100] C. 42, 47, 23, 100 D. No clue

25 Mutability: Lists are mutable In [1]: my_list = [42, 47, 23] In [2]: my_list = my_list + [3] In [3]: my_list Out[3]: [42, 47, 23, 3] In [4]: my_list.append(15) In [5]: my_list Out[5]: [42, 47, 23, 3, 15] In [6]: x = my_list In [7]: x.append(234) In [8]: x Out[8]: [42, 47, 23, 3, 15, 234] >>> my_list A. [42, 47, 23, 3, 15] B. x C. [42, 47, 23, 3, 15, 234] D. No clue

26 Types of data in Python: A growing list >>> goodnum = 42 >>> pi = Integer Floating point number >>> special = [2.718, 3.141, 42] >>> okfood = spam >>> greatfood = chocolate >>> 5 > 6 >>> False List String (single or double quotes work) Boolean (coming attraction)