Bioinformatics Analyzing High Throughput Sequencing Data
Bioinformatics Analyzing High Throughput Sequencing Data BMMB 597D
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This 0 page Class Notes was uploaded by Lou Koepp on Sunday November 1, 2015. The Class Notes belongs to BMMB 597D at Pennsylvania State University taught by Istvan Albert in Fall. Since its upload, it has received 18 views. For similar materials see /class/233086/bmmb-597d-pennsylvania-state-university in Molecular, Cellular And Developmental Biology at Pennsylvania State University.
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Welcome to BMMB 597D Practical Data Analysis for Life Scientists Istvan Albert Huck Institutes for the Life Sciences Information about the course Course webpage httpwwwpersonapsueduiua1 Office hours MW 23pm iua1psuedu Homework due Thursday the week after it was given out TA Zhenhai Zhang zv25012psuedu TA Zhaorong Ma zum112psuedu Rationale for this course Life sciences are becoming a data driven science Data is represented as text files in various formats Computational classes are usually focused on computer science algorithms We will focus on information processing Lecture topics 15 weeks two lectures per week 5 weeks computational foundations 3 weeks biological data formats 3 weeks statistical methods and visualization 3 weeks software tools 1 week presentations We will discuss multiple issues at once Lecture formats A main topic each week Practical examples that tie in with the topic Finishing with in class exercises depending 0 the subject Project formats The best motivator is doing something useful for yourself Let s solve some of your problems Send me a proposal on what type of data analysis would you like to see We will try to tailor the course to cover those topics in the second half of the semester Project example 1 We have microarray data and sequencing data for a certain organism 2 We d like to correlate gene expression values with sequencing read coverage around certain genomic markers Then you need to bring data either already published ones or a small percentage of unpublished data always ask permission from your advisor Expectations You can only learn by doing Spend 23 hours outside class each week Explore behaviors Expand the scope of the study Try new solutions Time flies when you know what you are doing Good News There is no other domain of knowledge where simply exploring experimenting leads to immediate and dramatic improvement in one s abilities Computation Thought Computational approaches reflect the thought process When we learn informatics we learn how to think in a way that is easy to translate into computation There is no magic it is just like any other subject matter Computers speak a different language It is called a programming language But designed by humans No wonder there are thousands of programming languages each reflecting someone s ideal on how things should really work Common traits A problem that can be solved in one particular programming language can be solved in any other computational language Are programming language all alike Not quite the same 34 problem that can be solved in one particular programming language can be solved n any other computational language The actual solution may be substantially different elm senememepp I e mm me new s 1ngl argz smnutpr1nlnlquotellc axial i 39 a szlaquot The cogni ve overhead may be very different Time to solution Two things determine time to solution How long it takes to create this solution human time How long it takes that solution to execute machine time Different languages make different tradeoffs Highlevel languages allow individuals to express their thoughts more quickly but the more abstract the language the more slowly it runs Food for thought What makes computers so inhuman They always do exactly what we tell them to do Often we re not sure what we ve actually said to the computer What is Python A simple but not simplistic programming language Very popular in certain sciences Named after the Monty Python comedy group not the snake What is Python for We will use it to interact with data Extract information Filter datasets Automate tasks Create charts Transform datasets for other bioinformatics tools Not really about Python This course isn39t really about Python It39s about solving data analysis problems But we have to write the examples in something Might as well choose something useful And it puts everyone on an equal footing We want to build skills that are transferable Sources of information All things Python httpwwwpythonorg Software carpentry httpsoftwarecarpentryorg some slides were be based on material from this lecture series this lecture series is for those who already know how to program Intermezzo Goal set up a process where tasks can be performed here in class The idea is to see right away when something does not make sense Python fundamentals Understand the basic building blocks 1 Every object has a tyge 2 Every object has a name1 Today s main lesson in one sentence When you have a problem check the type and the name 1 Unassigned expressions are allowed but in practice we always name them 143 gm us Eillie Edit Eadie ew Emjlect Tanking Ioolis hndiow Help 4i SENSE Him 5 Bugle Ema MW 397 age23 Iprint age print typeage rrr u r J Command Dutp ut I i x pythun 139 C 39 alher sauquotbkpp week testpy2 returned E Ln 2 Cal 1 Pythun More types and names Ens gm gm Mew 2mm mum 1m mumer FE 39 39Dm ah s vOf m1 swag quotMm 1 age23 2 weight1999 3 prod age weight a 4 print age typeage 5 print weight typeweight 5 print prod typeprod 7 v mm ampu v python rt C zygwmhumewabensuu bpptweek1testpy2gtMWEtumed u E 23 type 39int39gt 1999 type 39float39gt 23999 type 39float39gt ASCII Lamzz Unexpected problem Integer division i il hi Erie gm gm Mew Evmen 1mm 1m windullv Dimiiii clip a Qg i 5m Pagii 2m x i 7 age23 weight1eea prod age196 weight 5 print age188 typeage print prod typeprod lmu39lwaH iiumm aw pythonrt kygmemmeMaibeanu bpptweeidtetpylgtamplreturned gt 96 type 39float39gt m Ascn Ln 5 cm 1 Python Learn to recognize it There is a zero in my cata soup Solution don t use integers instead of real float numbers iuiEIinwi Eiie gm gm Mew 2mm Tonibo ionis window e 5 39DwDE JEJC La o swag kiwi 1 age23 weight 199 a imm Mimi if i x mm 4 39ygwinHameiaibensuu bpptweeidtest gym vetumed u a 923 type 39int39gt 239 type 39float39gt A501 Ln 6 cm 15 mm This you ll often see this error E Er g 232 py LCzygwrnhumerabenjamcesrabertrwebwp weekl r Kamoda m s 1 ENE gm gode y ew Ewen mm rams mdnw 4a 1 m 39 1 rm rpm 1 greeting quot Hello World quot 2 3 print greetings A v gmm mun Wm 7 WWmmmammWammrwgmppgwsgmm pybm mm 1 Traceback most recent call last File quotCcygwinhomeia1bertsourcesialbertwebppt week1testpyquot l39 in modulegt print greetings NameError name 39 reetings39 is not defined Ln 3 cm 15 Pyzhnn Ready Just about all data starts out as a string type Tame mm 1 fu11nam quotJoh 2 print fu11name 3 4 n type fu11name jam m pyttmn 4 wwonmewwbenmmsvsbemwemppnweemm pybm mm u John Doe type 39str39 7 Ready A501 Ln 1 cm 33 Pythun Some objects already know how to do certain tasks Python has introspection we can ask it to tell us what an object can do 1 The function that does this is called 2 Moreover we can always find more information by invoking the helg More about string attributes here dueto large fonts 1 testpy CEygwmhumeiaibemscmvte iaibemwempp weekl e Komuda m s 1 t i El Eiie Edit gees Mew men Taeim Innis indaw 6E v D31 7 i i 39 imimi if 1 greeting quotHello Worldquot 4 i 2 print dirgreeting f item umpmi These are the attributes of interest hymen 7 CygwiquotHameiaiben wvze iaibenrwebpptweeidtest py pm vetumed u use 1 39 39 39 sd 39 51 r39 391sspac 39 391stit e39 39isup er join 39ljust39 39lower39 39lstrip39 par tition J 39replace39 39rfind39 39rindex39 rjus 39rpartitlon39 rspllt39 39r str ip39J split 39splitl 39 39star 5 ith39 s 1 39swapcase39 39titl 39 39tr anslate39 39upper39 I39 zfill39 Check for these attributes on the previous slide 1 EN 4 s a 2 print greetinglower 3 print greetingupper 4 hello world HELLO WORLD This does not work Why g 52 py czygwmumm2managrammmxbemwempmmm r Kamudu m 5 w mm mm 1m mm e p V V EH3 gm gods 2 Elm quotIa D 5 mwmw 1 greeting quotHello Worldquot 2 print greetingrep1ace 3 Wm WM pythan 7 xEygwxnhumzabzn aurzEsa b nerMppt waEldVEn pyzgtm returned 1 Traceback most recent call last File quotC 1539 39 line 2 in ltmodulegt print greetingrep1ace TypeError replace takes at least 2 arguments a given u w AAAu Find out more about the replace attribute g 16thCEygWmhomeabeM513uvtesha benrwempp weeklr Komoda m 5 1 El EH3 Em gm Mew 2mm mum 1m mdaw ie p GHQ 37m smpage new A T 1 greeting quotHello we 1d 2 print helpgreetingrep1ace quot m femmmmu hymn 7 Czygwmhumeahenbauvesabemwebpp weeldtest py pm vetumed a He p on builtin function replace replace Srep1ace old new count gt string old replaced by new If the optional argument count 1 given only the first count occurrences are replaced Return a copy of string 5 with all occurrences of substring s Ready L4 A501 Ln39 3 cm 1 Pythnn Now we know the correct use case aw X EJE EJM 2 print greetingrep1ace39WOrld39 39Universe39 Hello Universe BMMB 597D Practical Data Analysis for Life Scientists Lecture 2 Istvan Albert Huck Institutes for the Life Sciences More on projects Two step process 1 Send me a description of the type of data analysis you are interested in a few paragraphs by the first week of October 2 In the last two weeks give a 510 minute presentation describing the data and some ofthe data analysis methods that have to be performed to extract what you need 3 We re not looking for a presentation of the scientific results Finalizing your setup Let s make sure everyone can run the examples MS to the rescue Komodo Edit has huge number of features Important features Line numbering syntax coloring key bindings Homework By this time next week perform every Python example that was presented in both lectures Type them in run them and see the output yourself Honor code based You can download larger slides from the web updated screenshots to large fonts Next Thursday turn in a sheet of paper with your name on stating that you ve done the exercises Today s topic are numbers Every data analysis task ends up manipulating numbers in some fashion There are some properties that we need to be aware of Most of the time they work as you think they should When they don t very frustrating and makes on feel powerless Revisit a previous example a b18 print ab print 19 ab print ab 1d If it leads to such subtle errors why is there a distinction at all Why can39t we have a single quotnumberquot type that always does the quotright thing Short detour Excel worksheet T 6982 692 2 0 062 3 Summing up the columns above 4 6982 6982 wme A1AZBI BZ gt a Type the formula A1A27B17B2 in the box What does it show Make sure cel number formatting set to Generaquotnot rounding Same problem now with Python 2 9 1 692 2 9 print A1 A2 Bl 32 What does it show Tell me These are representation errors Not all numbers are affected a b 95 print repra print reprb 919999999990969091 05 The actual representation for 01 O1000000000000000055511151231257827021181583404541015625 More information details at httpdocspvthonorgtutorialfloatingpointhtml And many other resources Not required for the course more for your personal enlightenment Our data already has errors Multiple orders of magnitude larger than the representation error So you are fine Usually There is one rule to remember Never compare floating point numbers for equality Integer comparison are exact 6929 62 a b c print 3 b c Use the as equality operator Float comparison are not exact 5929 862 a b c print 3 b c How do we compare floats print absdiff lt 15 1d I know It seems more work than it should be Other traps when using floats Care must be taken when combining numbers of widely different magnitudes It is not absolute sizes but relative ones 1 vs 1000 billion 1 vs 1000 billionth fraction Back to Excel smEv v x 1 I Auarm E I lobooool 1OEOE30A1BlBl 2 1 Type the formula A1B17B1 into the box What does it show 3 x Same operation with Python a b 1E39 print a b print a b b f What does it show See foryourself Integer computation works as expected 1232 py CEygwtnhumealber jauvuSVa benrwepr wrekl r Kamodau m 51 EBB bl He m gods mew gmjenjmm Ina si mdaw e p tathX V 1 these are comments the is the power operator a 196 b 1939 2 3 4 5 E you can put them anywhere 7 to document what you are doing 8 9 print typea a b p 39 t b b 4 m t r jammmom F x 1mm 7 AtygwxMnomevabemsouvzewa bemwempptweeldten py pm vetumed u type 39 int 39 gt 1999999 1999999999999999999999999999999 1999999 Ready 9 A50 Ln39 m cm 15 Python 7 Long Iooooong integers ELE p weekl r Komndg m 5 1 g leSLDy ckygwmmumamjp m we gm gm Ew mm mum e b m wmdw e p J GWYX 1 3 you can make them so huge 33 that it cannot finish computing 33 in a reasonabLe amount of time mmbw n on LB b w 0 print typea print a m Cammand Uutput pyzhon 7 Czygwimhome a bemwuvzesva benrwzbwp weeldtest py bm returned n on 39 1 41 5455194651 mum v 7 A50 Floating point conclusions Don t test equality for floats Use the size ofthe difference instead Don t put widely different magnitude numbers into the same formula Small numbers with small ones large ones with large ones Most problems naturally lend themselves to such processing Usually it is us who end up trying to be too smart and quotsavequot some time Casting between types We often want to transform one type to another type The process is called type conversion typecasting usually we just call it casting Python makes this simple use the same name that you found via the type function Casting in practice a print typea a 2 3 4 33 cast to fLoat 5 a floata typea a type 39str gt 123 lttype 39float39gt 1239 Casting back and forth may change values a print typea a 2 3 4 b floata 5 print typeb b 6 7 8 strb print typec c 39str gt 123 39float gt 1230 39str gt 1230 Some casts may fail This is good a print typea a b 2 3 in a 4 print typeb H 5 Traceback most recent call last File line 3 in module b ValueError invalid literal for int with base 16 39 Homework Help me cast this string to an integer What do I need to have In the code box to get the output below I type type a print typea a b floata c inth 39str39gt 1239 39int39gt 123 BMMB 597D r Practical Data Analysis for Life Scientists Week 3 Lecture 5 lstvan Albert Huck Institutes for the Life Sciences r slides marked as such contain more advanced concepts that are not 1 strictly required but good to know Standard Library Available by default with all python installations contain generic functionality such as built in functions simple math file access web access Global Module Index httQ4Zdocstahonorg4modindexhtml Very reliable tooset but mostly programming related users only need to e aware ofa small fraction External Libraries lnstallable into most python installations contain specialized functionality such as numerical methods charts and plotting bioinformatics graphs and networ Python Package Index PyPl httggZQZQiQZthonorgggxgi Quality not enforced and varies wildly across packages The Enthought Python distribution A python distribution that comes with several extension libraries ree for nonnprofit organlzations An experienced user Could Customize a Python installation to look like the Enthought Python distribution in afew urs work potential complications Pros convenient uniform everyone using the same libraries Cons you have to use older python version and possibly outdated external libraries 9102009 Organizing code program instructions 9 form a function multiple functions 9 form a module in a file many modules 9 form a package directory From functions to modules x def squarex turn x x 2 3 4 Create the square function and save the file under the name week3py The file we saved may be used as a module 1 The file name ends in py 2 The file name is a valid python identifier name ie contains only letters numbers not leading or underscore abcdpy 9 good Python1py 9 bad contains a minus sign 1233gXYShahoHNoyUcKpy 9 good technically speaking 1alphapy 9 bad leading numeral my codepy 9 bad contains a space week3py 9 good Using modules import name print typeweek3 print week3square2 l lttype 39module39gt 4 Create a new script then import the week3 module 9102009 Module compilation pyc week3py 9 week3pyc An optimization so that the module loads faster Will be recreated if we change the original file One catch When you delete a module you must also delete the compiled version of it pyc Using modules importing a function from the module square 2 3 print typesquare 4 print square2 lttype 39function39gt 4 The function square behaves as if were defined in the current script To import multiple functions separate their names with commas Import all functions from a module 2 3 print typesquare 4 print square2 lttype 39function39gt 4 Pros the imports all functions into the current script Cons you never know what has been imported gt Where is the function coming from print square2 what moduLe is function coming from print squaremodule W um MD WN introspection see aLL function attributes print dirsquare 9102009 9102009 Import path J Where does a module come from always adds the current folder estiyy x print week3file print week3square2 print dir weeksl I l Command Output W1th 2 CCygwlnhumEialbertmptWEek3tes ipy 2 m39 vetumed o 4 C cygwinhomeia1bertsourcesia1bertwebpptweek3week3 pyc 39builtins39 39 do 39 39 i 39 39 39 39 39 We can always import from the folder that the importing script is located in Import path 4 saving the script to another folder El 1 r r W p r a l El How to inform python to add a new folder to the python import path Import path general case Elle Edrt gode Mew Evoject Toolbox Ionls lndow Help l 51m paga madam 5114 X hwlpy a brief overview not required forthis class let me or the TA know If you want to set this up 1 import week H 2 TV 1 V 39 1 Set the environment variable PYTHONPATH to include the 7 directory JCDmmand ompm x python rt Ucygwinximmexiaihemsoures uaibmweb39ippmem pm lemme 57 Traceback most recent call last 2 Create a file ending in pth in the main import path that lists the File directories you want to a quotCcygwinhomeialbertsourcesialbertwebPPtte st1pyquot line 1 in lt dul gt import weeks ImportError No module named week3 Windows CPython25Li bsite packagesc ustompth Mac OS X LibraryFrameworksPythonframeworkVersions 430libpython25site packagescustompth Ready j ASCII Ln39l Cal 13 Python lmportError means Python cannot see your file un39x mgrhbpythonZ39SS39te39pakcageScustom39pth Name collisions will occasionally happen Example save a module as filepy then import it Elal E a Edrt gaaa Mew Erajecr Yuclbog Innis mnaaw ap Stan page weeBpy SEpr 52 x 1 import file 2 3 stream fi1e39data1txt39 Command 011pm returnzdl Traceback most recent call last i e quotCcygwinhomeialbertsourcesialbert webpptweek3 test2pyquot line 3 in ltmodulegt st e m file39data1txt39 TypeError 39module39 object is not callable Ready 2 Am Ln 3 BI 15 mm Adding documentation squarex quotReturns the squared inpu quot return x x Docstring documentation string Accessing help on module functions helpweek3squard Help on function square in module weeks squarex Returns the squared input Keep docs short simple and relevant Multiline documentation x def s arex Input Float or integer number Returns The squared valuelof the input return x x This is how multiline strings can also be created 9102009 Accessing long help on module functions helpweek3square Help on function square in module weeks squarex Input Float or integer number Returns The squared value of the input Keep docs short simple and relevant You should add comments as well the squared inputquot comments can go here return x x Document unexpected decisions Module level documentation El le gm gnde Mew Emjact Teama lame lnd w elp 1 L 2 Thislis a demo module for week3 3 4 It will be used to demonstrate Various 5 module specific functionalities 6 uquot 7 8 def squarex 9 Returns the squared inputquot 7 18 return x x 39 l Command amp 39 newnee 0 Pyth on Ready Add a string with information to the very beginning of the module j 39 39 39 W le gain genie Miew Emject Toulhog Innis induw Help sen Page weeklpy l testpr x import weeks 2 helpweek3 2 lmlavg 4 ml Tl Command 3qu gt 11 returned in Help on module week3 NAME weeks This is a demo module for weeks FILE 3week3py DESCRIPTION It will be used to demonstrate various module specific functionalities FUNCTIONS squarex ccygwinhomeialbertsourcesialbert webpptweek 9102009 Who do we write the docs for Cu rselves Tomorrow or next month the same task may look different and less obvioust You are helping yourself remember w at you did an and whyt When do we move functions into modules When the functionality reaches a generality that makes it reusable Module function goals 1 Simplicity try to make your functions fit in a single gage 2 Generalitx capture a reusable task 3 Well documented helps you remember what the function does Ultimate goal of each function Perform a single well defined task 9 General naming standards 1 expressiondata 123 9 variable names fused 2 expressiondata 123 9 variable names separated by underscore when long my preference 3 ExpressionData 123 9 variable names separated by so called CamelCase usually used for classes 4 expressionData 123 9 yuck 9102009 Homework 3 Part 13 Create a module Take the functionality that you wrote for Homework 2 and move it into a module that can be imported as import week3 A script shown on the next slide needs to be able to run with your module Document your functions and your module Turn in the module that you wrote next Tuesday Homework 3 Part 23 The script that must be able to run values week3readealues39dataZtxt39 print sumvalues 2 In class execrises 1 Let s do part of the homework Preparing for next lecture test that the following works import numpy BMMB 597D Practical Data Analysis for Life Scientists Week 3 Lecture 6 lstvan Albert Hucklnst utesforthelJ eSdences 9102009 9102009 Questions from last lecture Note the difference langg 3 39 39 mg Edit Cude Mew Erujecl Taming Innis mduw Help l sen Page t5templypy Sislideipy x E def greetingname 2 L print 39Hello 39 name 3 4 print greeting World39 name Hello 39 nama return text print greeting39World39 l Cummand Output rammed 0 E Hello World Hello World All functions return a value E x IICIt value return If you do not specify anything they wull return None p uestion on namin ob39ects Q g J Bad names don t do thIs variables functions parameters modules You can call them anything you want using the restricted alphabet 39 percentage return text Having parameter with confusing names can be very Confusing print calculate 39World39 It is your job to name them meaningfully Hello World Calling a variable something does not make it behave a certain way 1 2 3 4 Naming tips If it is a number you can call it value x y 2 age level If it is a string call it name id text gene sequence If it is a container lines values rows entries If it is a function then action oriented Verbs report generate read getvalues The better your names are the easier is to understand your m 1 2 More on errors Ever one makes programming errors all the time We cannot avoid making errors There is no silver bullet Solution What we need are the skills and an approach that allow us to solve errors very quickly Actually there is a silver bullet Simplicity A long program will have substantially more errors an a short one Disproportionately so Catch it is not easy to write s mple programs e tend to overcomplicate tasks Today we ll do lots of in class exercises It is important to be able to read a program and 39mentally39 execute small parts of it We will practice that shortly We will also do some parts of the newly assigned homework 9102009 10 Knowledge Masters slides to follow See if you can correctly predict what the program will produce 1 Predict the output or reason for the error 2 Run the program if possible and check the result 3 If the output is an error then write the program that creates that error 1 Homework 33 Knowledge Master 1 2 Keep practicing the slides that follow Turn in the solution for each slide Write the type of the output and the output itself If the example is an error specify the reason for getting that error Don39t turn in the programs that you may write but do create programs that generate the errors that you see Solution examples Slide 1 list type 1 23 Slide 2 incorrectly written parentheses missing the last one Homework du e next Tuesday with parts 1 and 2 from the previous lecture Knowledge Master 1 3 xesulid21 pyCygwinhumeialbemuresialbertrwebpptwe l E Eli Edi god Miew Erujzd Team Innis window Help 7Starl Page I tecrempcy zmsMepr x 1 ldef conditionx 2 return x lt 3 l 3 i 4 data 1 2 3 4 5 quot 5 6 print filtercondition data 7 v l 739quot i mm new i 1mmquot 7 CCygv linhamelalben ourctur lestrzmptypy 2gt m returned a Ln1 Cal 1 Pythun 7 Knowledge Master 2 g testslidelpy ceygwinhemezaxeeneemesxleibemwebxppzxw in l Erajitt Tuolbuz 1am xndaw Help def conditionx 2 return x lt 3 3 4 data 1 2 3 4 5 5 6 print maplcondition data Command 0 hymen 7 ltey9wmhumemlbemeeumeuresxxesremptyey 2 m returned a 9102009 11 Knowledge Master 1 return x lt data 1 2 3 4 5 data filtercondition data print mapcondition data 1 Knowledge Master 4 lismme licmemmw 5mm x Edit gang Mew 2mm rumba lunls mnduw Help import week3 l ummand Output returned 1 Traceback most recent call last File quotCcygwinhomeialbert ecture5testslide2pyquot import weeks File quotCcygwinhome ecture5week3p data values2 NameError name values is not defined sourcesialbert webpptweek3l lin in module ialbertsourcesialbert webpptweek3l yquot line 3 39 ltmodu1egt wmm Where would you look for the error What caused the error 9102009 Knowledge Master 5 j 39 39 39 5 gm gods mew gmjm Tnulbog Innis mndaw Help l StartPage tstrempxypy 555112pr x import week Command Output l 39 r returned 1 File 1 quotCcygwinhomeialbertsourcesialbert webpptweek37 lecture5testslide2py line 1 in ltmodu1egt imp ek3 File Ccygwinhomeialbertsourcesialbert webpptweek3gt lecture5week3py line 7 data2txt39 A SyntaxError EOL while scanning single quoted string Where would you look for the error What caused the error Knowledge Master 6 ElEH E g a 913 Mew Emjecc 70mm Incl mnduw zlp 1 5m page licmrmmm lts idelyy x l import weeks l mm amp l gt returned 1 Traceback most recent call last File quotCcygw lecture5testslide2py import week3 F inhomeialbertsourcesialbert webpptweek3 1i 1 in module File quotCcygwinhomeialbertsourcesialbert webpptweek3 lecture5week3py i value 2 x TypeError unsupported operand types for and 39 str39 in module Where would you look for the error What caused the error 12 9102009 Knowledge Master 7 g l E g r r l El amp 5 gm gods 39ew Emject Tnulbog 13m mndow ap 7 H 7 t guns mew 2mm Tomlin Iools Mndow ap l Start page t5bmptypy tasl39rde l mama x lv m c p testjideZqu x l 1 import week3 1 import week 4 l w r t l m J Cummand Outputl 39 X Command Output V v gt returned 1 7quot r gt rstumid 1 TracebaCk MOSt recent C311 135t Traceback most recent call last File File quotCcygwinhomeia1bertsourcesia1bert webpptweek3 1ecture5testslide2pyquot line 1 in mod gt import week3 quotCcygwinhomeia1bertsourcesialbert webpptweek31 ecture5testslide2pyquot 11 1 in d gt 3 1e quotCcy inhomeia1bertsourcesia1bert webpptweek3 1ecture5we mo u1e import wee ImportError No module named week3 ek3pyquot line 9 in module val x 2 TypeError cannot concatenate 39str39 and 39int39 objects Ready ASCII Python Ready 13 Python quot L Where would you look for the error What caused the error What caused the error How would you fix it Knowledge Master 9 Knowledge Master 10 2 data 1 2 3 4 3 print mapfloat data print data2 data 2 13 Knowledge Master 11 take your time with this one print data 2 p Slicing interval is closed on beginning and open at the end 9 Meaning that it includes first index but does not include the last indext Knowledge Master 12 gene pr39int gene3 pr39int gene 3 pr39int gene59 1 9102009 Knowledge Master 13 j 39 Ella Edit gage yew 2mm Tmle Innis mduw elp sum Page Stranptypy emuks x l 1 import weeks 0 7 Command Output K 39 39 39 39 returned Traceback most recent call last File quotC cygwinhomeia1bertsour cesia1bert webpptweek31ectur e5testslide5 pyquot line 1 in ltmodu1egt import week3 F quotC cygwinhomeia1bertsour cesia1bert webpptweek31ectur e5week3 pyquot line de 1 2 3 SyntaxError invalid syntax Pytth ady Knowledge Master 14 2 total 69 value 3 half total29 4 5 print computelt1ee 1 14 9102009 Let s do them one by one In class exercises Get a copy of the large version of the Knowledge Master slides 15