CSE 111 Bio: Program Design I Class 11: loops

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1 SE 111 Bio: Program Desig I lass 11: loops Radall Muroe, xkcd.com/1411/ Robert H. Sloa (S) & Rachel Poretsky (Bio) Uiversity of Illiois, hicago October 2, 2016

2 Pytho ets Loopy! he Pytho, Busch ardes Florida

3 outig 's def cout(str): """outs umber of characters i a strig""" cout = 0 if str[0] == '': cout = cout + 1 retur cout

4 for loop basic idea for c i st: <body that refers to c> execute body le(st) times, oce each with c beig each character of strig st i order (I geeral, st could be ay sequece, e.g., a list ad c is each elemet of st oce)

5 Example: d detector >>> d("i would like a dodecarchy i the US") 3 >>> d("i am agaist the letter after c") 0 def d(iput): couter = 0 for symbol i iput:

6 Example: d detector >>> d("i would like a dodecarchy i the US") 3 >>> d("i am agaist the letter after c") 0 We choose the ame of a variable def d(iput): couter = 0 ad we provide a sequece for symbol i iput: if symbol == 'd': couter = couter + 1 retur couter

7 his will prit? for x i "0123": prit(x). 0 D. 0 1 B E. his will 2 ru 3 forever

8 Recall ORF fidig problem Lab: heckig whether ucleotide sequece legit code (aka "Ope readig frame" or ORF): q Starts with the start codo () q Eds with oe of the stop codos (,, ) q Has legth multiple of 3 Really wat: From some (typically very log) sequece q q q Fid if ay cosecutive substrig has that property Fid the first or logest or shortest or substrig with that property Fid all the substrigs with that property, ad put them i a list for the biologists to pick out the oes that have ice biological properties

9 Fidig a ORF i a very short strig Modify our orf_advisor() fuctio's retur values to be q q rue if legit ORF False i all other cases Mildly less useful iformatio tha what we assiged you as lab, but makes fuctio more useful as subroutie goig for the more geeral problem very easy chage to make to the assiged program all the ew oe orf_advisor2() just to kow we mea it (the oe with oly 2 possible retur values)

10 Fidig existece of ORF i very short strigs def exists_orf(da): if le(da) == 6: retur orf_advisor2(da) if le(da) == 7: if orf_advisor2(da[0:6]) or orf_advisor2(da[1:7]): retur rue else: prit("sorry, ca't help you")

11 Or eve legth 9 strigs def exists_orf(da): if le(da) == 6: retur orf_advisor2(da) if le(da) == 7: if orf_advisor2(da[0:6]) or orf_advisor2(da[1:7]) retur rue if le(da) == 8: if orf_advisor2(da[0:6]) or orf_advisor2(da[1:7]) or orf_advisor2([2:8]): retur rue if le(da) == 9: if orf_advisor2(da[0:6]) or orf_advisor2(da[1:7]) or orf_advisor2([2:8]) or orf_advisor2([3:9]): retur rue else: prit("sorry, ca't help you")

12 But his will be a real drag eve for 40 ucleotide rus Imagie 15,000 characters.... We eed for loops q for loops allow us to do same thig for every item i a sequece! ORF is pretty complicated, because we really wat to cosider all subsequeces ot just each character i sequece q q Will come back to it For ow: You're doig so well, how about a complemet?

13 Example: omplemet of DN Sequece Suppose we are assiged to write a fuctio that takes a DN sequece as iput ad returs the complemet Fuctioal decompositio: q q Build up the complemet by For each ucleotide i the sequece et its complemet (hmm, we'll eed a fuctio for that) dd that complemet to the aswer

14 Desig & implemetatio strategy hik about the problem ad desig your attack "top dow" as we did o previous slide Implemet the fuctios oe at a time, startig with fuctios that do ot call other fuctios q I.e., "bottom up" So, for this problem start with complemet fuctio q d we hope you fiished it already i lab yesterday!

15 complemet() def complemet(): """Returs -/- complemet of iput uc.""" # Would be straightforward as a lab assigmet # But some dar professors might worry # that complemetig to mrn ivolves Uracil (U)

16 ive complemet fuctio def comp_seq(da): """returs complemet strig of DN seq da""" aswer = "" for uc i da: aswer = aswer + complemet(uc) retur aswer

17 ommo programmig patter Iitialize a aswer q Ofte to 0 for umbers, "" for strigs, [ ] for lists Build up aswer i a for loop Retur aswer after ad outside of for loop

18 PRORMMIN SYLE & DESIN

19 Some Notes o Programmig Style Remember: ode eeds to be uderstood by both computers ad people Should try to make code as easy to read as possible Pro tip: his will make it easier for s ad profs to give you partial credit o assigmets, exams, etc.

20 ood Pytho Programmig Style Meaigful variable & fuctio ames q q eerally startig with lower-case letter Pytho style is _ betwee "words" i ame; hece orf_advisor (ot orfdvisor) Blak lie betwee fuctios Use of docstrig to briefly describe iput-output behavior of fuctio d, of course, be very careful with idetatio

21 Program desig: Fuctios Some laguages, e.g., Java, ++, build everythig aroud classes (ad objects ad methods) I Pytho, most commo buildig block of desig, ad oe we'll use i this course: fuctios q So we wat to be really good ad kowledgeable about fuctios

22 FUNIONS: REVIEW HEN PRMEERS (YE MORE ON FUNIONS)

23 Fuctio as Iput-Output box Fuctio: akes oe or more values i (i geeral; we sometimes use fuctios of zero iputs) q Parameters! More shortly More ofte that ot, fruitful: retur a value q q q So, if we're oly usig the fuctio, we ca thik oly about it as a iput-output box More ofte, we're writig the fuctio But we still eed to start by uderstadig the iput-output box behavior

24 What does retur do that prit does ot returs a value to the caller stops executio of the program

25 fuctio of 1 parameter igorig its iput returig 42 def weird(poor_igored_iput_parameter): retur 42 weird poor_igored_iput_parameter 42

26 Parameters (1) (actual) parameter I [1]: y = abs(-3) I [2]: y Out[2]: 3

27 Parameters (2) Parameters i the ()s i def statemet called formal parameters Formal parameters are (like) variables : they're the thig that chages iside the fuctio Fuctios have 0 or more parameters Value(s) i fuctio call: actual parameter(s) q q Same umber as formal parameters ould be variables ad/or literal values

28 Parameters ad fuctio executio Like fuctios i high-school lgebra 2: q t time fuctio called, formal parameter takes o value of actual parameter lgebra 2: q if f(x) = 3x, the 4 + f(20) = 64 ad implicitly at least, the formal parameter x took o the value 20. Pytho: 4 + triple(x) q formal x boud to 3 for legth of ru of triple()

29 I eve more detail def triple(x): retur 3 * x formal parameter >>> 4 + triple(20)

30 I eve more detail def triple(x): retur 3 * x formal parameter x boud to 20 >>> 4 + triple(20) t poit where triple(20) is called, value 20 is assiged to triple's iteral x parameter, multiplicatio is doe gettig value 60, umber 60 is retured (ad triple is doe), ad iterpreter (commad lie) adds 4 ad 60

31 Formal vs. actual parameters def triple(x): retur 3 * x formal parameter >>> = 17 >>> triple() 51 >>> 4 + triple(20) 64

32 Formal vs. actual parameters def triple(x): retur 3 * x formal parameter (which happes to be x i this example) >>> = 17 >>> triple() 51 >>> 4 + triple(20) 64

33 Formal vs. actual parameters def triple(x): retur 3 * x formal parameter >>> = 17 >>> triple() 51 >>> 4 + triple(20) 64 actual parameter

34 RNE

35 Idea of rage() For complicated walkig over sequeces, like ORF frames, we ofte eed to do mildly complicated thigs ivolvig possible idices. E.g., for all possible startig letters i seq: for all eds givig substrig legth >= 6 ad multiple of 3: see if it's a ORF Would be ice to have way to get list of umbers for for loop to go over

36 Idea of rage (cot.) (actually slightly differet) >>> rage(0,25) [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] >>> rage(25) # same thig assume start poit of 0 [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] >>> rage(3,9) [3, 4, 5, 6, 7, 8] >>> rage(3,15,3) [3, 6, 9, 12]

37 his will prit? for x i rage(4): prit(x). 0 D. 0 1 B E. his will 2 ru 3 forever

38 rage fuctio rage(start, stop) gives somethig a for loop ca walk over, goig from iteger start up to but ot icludig iteger stop (like slices!). E.g: for i i rage(0, 25): prit(i) # prits out 0, 1, 2,, 24

39 For Pytho laguage lawyers (or S 341) echically type of output of rage is rage, a kid of iterator (take S 341 for more ) If you wat the list, use list(rage(start, stop)) E.g., >>> list(rage(0, 25)) [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] >>> rage(0,25) rage(0,25)

40 First example of explicit type coversio ame_of_type(object) coverts object to ew object type with "same" value, where that is sesible I [1]: list(rage(4)) Out[1]: [0, 1, 2, 3] I [2]: list("cat") Out[2]: ['c', 'a', 't'] I [3]: it(3.55) Out[3]: 3

41 What do we get from it("cat"). he legth of "cat" (i.e., 3) B. Iteger code for c. error D. No clue ValueError: ivalid literal for it() with base 10: 'cat'

42 ENE FINDIN (ORFS)

44 ee predictio why? Determie the fuctio ad evolutioary origi of gees Piece together gees from sequecig fragmets Detailed fuctioal aotatio of gees ad geomes Lear how gees are regulated

Sigma mrn start 35 regio osesus Pribow box Promoter sequece 5 3

47 Sigma mrn start 35 regio osesus Pribow box Promoter sequece RN polymerase (core ezyme) rascriptio

48 Figure 9.18 Eukaryotic mrn cotais itros that must be spliced out. 5' cap ad 3' tail are also added.

49 ee predictio how? his is a major area of iterest i computatioal biology Use codo usage frequecies, look for kow ORF patters = b iitio methods Probabilistic models (like Hidde Markov Models) Look for sigificat matches of query sequece with sequece of kow gees = Homology methods

51 % otet Bias he four bases (,,,) are geerally ot preset i equal proportios i geomes ot eve close! I most orgaisms they are preset i equal = & = ratios But vs. ratios ca also vary widely ad do. I the majority of eukaryotes, % > % cotet Usually, we arbitrarily keep track of % cotet, by covetio - Huma geome, = 41% - almost all orgaisms betwee 25% - 75% % cotet also varies withi geomes; specifically, % cotet is higher withi codig regios (gees)

CS 111: Program Design I Lecture # 7: First Loop, Web Crawler, Functions

CS 111: Program Design I Lecture # 7: First Loop, Web Crawler, Functions CS 111: Program Desig I Lecture # 7: First Loop, Web Crawler, Fuctios Robert H. Sloa & Richard Warer Uiversity of Illiois at Chicago September 18, 2018 What will this prit? x = 5 if x == 3: prit("hi!")