CSE111Bio:ProgramDesignILecture5:MoreStrings,IntroLists,Translation&Central

DogmaofBiology

RobertSloan(CS)&RachelPoretsky (Bio)UniversityofIllinois,Chicago

September12,2017

Whatdoesthiscodeprint?

x = "Go"y = "Flames!"print(x + y)

A. Go Flames!B. GoFlames!C. ErrorbecausetheadditionisillegalD. Go

Admin:Midterm1nosoonerthan9/28

•Midterm1moved.Thursday9/28• (slightlytentative,couldbealittlelater)

•Wereallydon'twanttoscheduleanyhourexamonadaywhenastudentwillbeoutforareligiousholiday—sowedidthatPiazzapoll

Review:Indexingstrings

• [i]afterstringgivescharacternumberi• Important:Python(andmanycomputerscientists!)countsfrom0,notfrom1!

• After:my_DNA = "AATGCCGTGCTT"• my_DNA[2] à 'T'

0 1 2 3 4 5 6 7 8 9 10 11A A T G C C G T G C T T

Negativeindices

• Sometimeswewanttogetourhandsonthelastcharacterofastring• Oneway:my_DNA[len(my_DNA)– 1]• Whyisthat– 1inthere?• Becausemy_DNA stringhas11characters,solength11,butcharactersnumbered0,1,2,…,10andingeneralthecharactersofstringsarenumbered• 0,1,…,len(s)– 1

Negativeindices

• Sometimeswewanttogetourhandsonthelastcharacterofastring• Oneway:my_DNA[len(my_DNA)– 1]• Another,ofteneasiertothinkaboutway:• Index–1isalwayslastcharacterofstring• Andindex-22nd lastcharacter,andsoon• Somy_DNA[-1]à 'T';my_DNA[-3]à 'C'

0 1 2 3 4 5 6 7 8 9 10 11A A T G C C G T G C T T

Slicing:Gettingpartofastring

• Substringofastringiscalledslice• s[m:n]returnscharactersfromindexm(countingfrom0asalways)uptobutnotincluding charactern

bt = "Dr. Rosalind Franklin"0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0

bt[0:3] à 'Dr.'bt[4:12] à 'Rosalind'

Slicing:omission=start/end

bt = "Dr. Rosalind Franklin"0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0

bt[:12] à 'Dr. Rosalind'bt[13:] à 'Franklin'

andsortofsillyone:bt[:] à 'Dr. Rosalind Franklin'

Trivia:Overendtreatedasend

>>> s = "Register to vote!"

In [1]: s[9:11]Out[1]: 'to'In [2]: s[12:20]Out[2]: 'vote!'

0 1 2 3 4 5 6 7 8 9 1 1 1 1 1 1 1 0 1 2 3 4 5 6

Usingstrings:slicing(Recap&check)

>>> myDNA = "AATGCCGTGCTT"

>>> myDNA[0:4]

>>> myDNA[3:7]

>>> myDNA[1:]

>>> myDNA[:4]

A A T G C C G T G C T T0 1 2 3 4 5 6 7 8 9 10 11

'AATG'

'GCCG’

'ATGCCGTGCTT'

'AATG'

TGCTT ?

A. myDNA[5]

B. myDNA[7:11]

C. myDNA[7:12]

D. myDNA[7:len(myDNA)]

E. No clue

Fancyslicingyou'llalmostneveruse

• Youareallowedtogive3indices,whichareinterpretedasstart:end:stepbt = "Dr. Rosalind Franklin"

012345678901234567890bt[4:17:3] à RanFn'

Strings:lotsofotherthingtoo!(Labhint!)

• Stringshavemanybuilt-into-Pythonmethodsfordoinglotsofusefulthings.Willcoverindetailinnextfewweeks.Oneexamplefornow:• Countingoccurrenceofletter(oranysubstringinastring):withthe.count()stringmethod:• sentence = 'Mary had a little lamb'• sentence.count('a') à 4• sentence.count('had') à 1• sentence.count('T') à 0

Somepeople objectsjustneverchange

• InPython,integersareimmutable• Cannotassignto integerobject• I.e.,cannotwrite1=0• Probablynotasurprise

• Important:stringsareimmutable too!

first_codon = "ACT"first_codon[0] = "G" Illegal; ERROR!

ButProfessor

• Canwriten = 1n = 0

• Isthatchanginganinteger?

ButProfessor

• Canwriten = 1n = 0

• Isthatchanginganinteger?• NO!Changingwhichobjectvariablenamenisassignedto• Couldreassign(entireobjectof)first_codon too

Pictures

1

Someimmutableobjectsinmemory

'ACT'

nfirst_codon

Pictures

1

Someimmutableobjectsinmemory

'ACT'

nfirst_codon

0

n=0doesn'tchangeimmutableinteger1,justtheassignmentofavariabletoanobject

Pictures

1

Someimmutableobjectsinmemory

'ACT'

nfirst_codon

0

first_codon =0doesn'tchangeimmutableinteger1,justtheassignmentofavariabletoanobject

Problemwithfirst_codon[0]='G' Someimmutableobjects

inmemory

'ACT'

first_codon

first_codon[0]="G"illegalbecausecannot changecontentsofany blueboxes.Thoseobjectsareimmutable

Comingattractions:Mutabletypes

• Numbers,Booleans,andstringsareallimmutable• Pythondoeshavesomemutabletypes• Twoveryimportantoneswewillseeare• Listsanddictionaries

Lists:BriefOverviewSlowerwithmoredetailscoming

Lists

>>> primes = [2,3,5,7,11]

>>> biologists = ["james","francis","rosalind"]

>>> L = [2, ”zebra", 11]

>>> M = [2, ”zebra", 11, ["spam","spamity","spam"] ]

Listsindex/slicethesameasstrings>>> 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"]

0 1 2 3

Additioninlists>>> my_list = [42, 47, 23]>>> newList = my_list + 100BARF!>>> 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

Mutability:ListsaremutableIn [1]: my_list = [42, 47, 23]In [2]: my_list = my_list + [3]In [3]: my_listOut[3]: [42, 47, 23, 3]In [4]: my_list.append(15)In [5]: my_listOut[5]: [42, 47, 23, 3, 15]In [6]: x = my_listIn [7]: x.append(234)In [8]: xOut[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

TypesofdatainPython:Agrowinglist>>> goodNum = 42

>>> pi = 3.1415926

>>> special = [2.718, 3.141, 42]

>>> okFood = “spam”

>>> greatFood = ‘chocolate’

>>> 5 > 6>>> False

Integer“Floating point” number

List

String (single or double quotes work)

Boolean (coming attraction)