Introduction to Programming

1. Introduction to Programming • A program is a sequence of precise instructions • Common programming languages: Python, Perl, Java, C++ • Elements of a programming language: • keywords – words that have special meaning (the vocabulary) • syntax – rules that describe the valid constructs (the grammar) • Some of the keywords in Python if else def elif for return in

2. Python Environment • Python Shell: for executing and testing the programs • Python Editor: for typing/creating the programs

3. Introduction to Python • Using Python as a fancy calculator >>> 2 + 3 5 >>> 2 + 3 * 4 14 >>> (2 + 3) * 4 20 >>> exams = 100 >>> labs = 70 >>> total = exams + labs >>> print total 170

4. Functions • Adding your own constructs • describe how to convert from Fahrenheit to Celsius To CONVERT to Celsius a given temperature: 1. subtract 32.0 from the given temperature 2. multiply the value from step 1 by 5.0 3. divide the value from step 2 by 9.0 4. report the value from step 3 defconvert(degrees): value1 = degrees - 32.0 value2 = value1 * 5.0 result = value2 / 9.0 return result

5. Functions • Adding your own constructs • describe how to convert from Fahrenheit to Celsius defconvert(degrees): value1 = degrees - 32.0 value2 = value1 * 5.0 result = value2 / 9.0 return result • Testing the new construct (in the Python Shell): >>> convert(32) 0 >>> convert(-40) 170

6. Functions • Adding your own constructs • describe how to convert from Fahrenheit to Celsius defconvert(degrees): value1 = degrees - 32.0 value2 = value1 * 5.0 result = value2 / 9.0 return result • The first two keywords – def and return: • def– define a new construct • return–computation is done, send the "result" back

7. Variables • Adding your own constructs • describe how to convert from Fahrenheit to Celsius defconvert(degrees): value1 = degrees - 32.0 value2 = value1 * 5.0 result = value2 / 9.0 return result • A new concept – variables: • places to store values • keep track of intermediate quantities • Variable names can be anything (other than keywords) but: • must contain only letters, digits, and _ symbol • cannot start with a digit

8. Functions • Adding another construct • describe how to compute the average of two numbers To compute the AVERAGE of two numbers x and y: 1. Add the numbers x and y 2. Divide the value from step 1 by 2.0 3. report the value from step 2 defaverage(x, y): total = x + y result = total / 2.0 return result >>> average(20, 70) 45 >>> exams = 90 >>> labs = 80 >>> average(exams, labs) 85

9. Functions • Multiple steps can be carried out at once defaverage(x, y): total = x + y result = total / 2.0 return result defaverage(x, y): result = (x + y) / 2.0 return result defconvert(degrees): result = (degrees - 32.0) * 5.0 / 9.0 return result defconvert(degrees): value1 = degrees - 32.0 value2 = value1 * 5.0 result = value2 / 9.0 return result

10. Functions Summary • Functions describe useful computations • Functions take input, process the input, and return a result convert average

11. Functions Summary • Choose good names for the function, inputs, and variables defaverage(x, y): result = (x + y) / 2.0 return result defcompute(tic, tac): toe = (tic + tac) / 2.0 return toe

12. Expressing Decisions • Write a function that computes absolute value of a number To compute the Absolute Value of a given number x: 1. if x is greater than 0: the result is x itself otherwise: the result is negative x 2. report the result defabsValue(x): if x > 0: result = x else: result = -x return result >>> absValue(5) 5 >>> absValue(-3) 3

13. Chaining Decisions • Write a function that converts a student’s exam score to a grade in the range [0 .. 4] To convert a given exam score to [0..4]: 1. if the score is at least 90: the result is 4.0 otherwise if the score is at least 80: the result is 3.0 otherwise if the score is at least 70: the result is 2.0 otherwise if the score is at least 60: the result is 1.0 otherwise: the result is 0.0 2. report the result defcomputeGrade(score): if score >= 90: grade = 4.0 elif score >= 80: grade = 3.0 elif score >= 70: grade = 2.0 elif score >= 60: grade = 1.0 else: grade = 0.0 return grade defcomputeGrade(score): if score >= 90: grade = "A" elif score >= 80: grade = "B" elif score >= 70: grade = "C" elif score >= 60: grade = "D" else: grade = "F" return grade >>> computeGrade(93) 4.0 >>> computeGrade(68) 1.0

14. Decisions Summary • The new keywords:if, elif, else • Expressing comparisons if value1 == value2: if value1 <> value2: ... do something ... ... do something ... if value1 < value2: if value1 > value2: ... do something ... ... do something ... if value1 <= value2: if value1 >= value2: ... do something ... ... do something ...

15. Strings • Variables can contain strings (sequence of characters) course = "Bioinformatics" fragment = "GATTACA" • Representation course ---> • Accessing individual elements print course[0] displays B print course[1] displays i printcourse[13] displays s • Finding the length of a string len(course)

16. 5 (stop value) is not included Expressing Repetition • General form for variable inrange(start, stop): ... DO SOMETHING ... • Example >>> for iinrange(1, 5): print i 1 2 3 4 >>>

17. Expressing Repetition • Write a function that takes two inputs (low, high) representing Fahrenheit temperatures and displays the Celsius equivalents of all temperatures in between To print all Celsius temps. between the values low, high: 1. for each temperature in the range (low, high): 1.1. compute Celsius for current temperature 1.2. print the value from step 1.1. defprintCelsius(low, high): for f inrange(low, high): c = convert(f) print c >>> printCelsius(32, 40) 0.0 0.555 1.111 1.666 2.222 2.777 3.333 3.888 4.444

18. Repetition and Strings • Write a function that takes one input (a DNA sequence) and displays each individual character from the sequence To print the individual characters in a given DNA string: 1. for each indexin the range of valid DNA indices: 1.2 print the DNA character at the current index defprintBases(sequence): for index inrange(0, len(sequence)): print sequence[index] >>> printBases("GATTACA") G A T T A C A

19. Repetition and Accumulation • Write a function that takes one integer, n, as input and returns the sum of all integers from 1 to n. To add the integers from 1 to the given number n: 1. for each number in the range from 1 to n: update the total sum byadding the current number 2. report the total sum To add the integers from 1 to the given number n: 1. set up a blank variable for the total sum 2. for each number in the range from 1 to n: update the total sum byadding the current number 3. report the total sum >>> addIntegers(5) 15 >>> addIntegers(6) 21

20. Repetition and Accumulation • Write a function that takes one integer, n, as input and returns the sum of all integers from 1 to n. To add the integers from 1 to the given number n: 1. set up a blank variable for the total sum 2. for each number in the range from 1 to n: update the total sum byadding the current number 3. report the total sum defaddIntegers(n): total = 0 for numberinrange(1, n): total = total + number return total

21. Executing a Program Line by Line

22. Computing GC Content • Version I with two counters – one for G’s and one for C’s defcomputeGCcontent(strand): countC = 0 countG = 0 for index inrange(0, len(strand)): if strand[index] == "G": countG = countG + 1 elifstrand[index] == "C": countC = countC + 1 content = 100.0 * (countG + countC) / len(strand) return content

23. Computing GC Content • Version II with one counter for the total of G’s and C’s defcomputeGCcontent(strand): countGC = 0 for index inrange(0, len(strand)): if strand[index] == "G": countGC = countGC + 1 elifstrand[index] == "C": countGC = countGC + 1 content = 100.0 * countGC / len(strand) return content

24. Computing GC Content • Version III with one counter using the or keyword defcomputeGCcontent(strand): countGC = 0 for index inrange(0, len(strand)): if strand[index] == "G" or strand[index] == "C": countGC = countGC + 1 content = 100.0 * countGC / len(strand) return content

25. returnvsprint • return sends a value back that can be stored and used • print only displays a value on the screen defaverage(x, y): result = (x + y) / 2.0 return result >>> labs = average(2.0, 4.0) OK >>> grade = labs + average(3.3, 3.6) OK defaverage(x, y): result = (x + y) / 2.0 print result >>> labs = average(2.0, 4.0) Nothing to store!! >>> grade = labs + average(3.3, 3.6) Nothing to add!!

26. returnvsprint • return sends a value back that can be stored and used • print only displays a value on the screen • In functions typically should usereturn • Remember that returnterminates the function immediately; put return at the point where the result is ready to report

27. Decisions Revisited • The else portion is not mandatory: if base == "A": count = count + 1 else: count = count • This is fine – if the condition fails, we simply do nothing: if base == "A": count = count + 1 no need

28. Decisions Revistied • Difference between if-elif-elif(chained if) vs. if-if-if What is the result from computeGrade(80)? defcomputeGrade(score): if score >= 90: grade = "A" elif score >= 80: grade = "B" elifscore >= 70: grade = "C" elif score >= 60: grade = "D" else: grade = "F" return grade defcomputeGrade(score): if score >= 90: grade = "A" ifscore >= 80: grade = "B" if score >= 70: grade = "C" ifscore >= 60: grade = "D" else: grade = "F" return grade

29. 5 (stop value) is not included Repetition Revisited • General form for variable inrange(start, stop): ... DO SOMETHING ... • Example >>> for iinrange(1, 5): printi 1 2 3 4 >>>

30. Repetition with Skips • Adding a step to skip at regular intervals(optional) : for variable inrange(start, stop, step): ... DO SOMETHING ... • Example >>> for iinrange(1, 9, 2): printi 1 3 5 7 >>> Same outcome for stop value of 8: >>> for iinrange(1, 8, 2): printi 1 3 5 7 >>>

31. Slicing Strings • Extracting portions from a given string (slices) course = "Bioinformatics“ course ---> printcourse[0 : 3]displays Bio printcourse[3 : 7] displays info printcourse[5 : 11] displays format print course[10 : 14] displays tics • In general course[start : stop] will extract all characters from index start up to (but not including) index stop

32. Skipping and Slicing • An example that uses skipping and slicing • write a function that prints the 3-letter codons in a given RNA >>> printCodons("GAUUACAUGAACGUU") GAU UAC AUG AAC GUU To print the 3-letter codons: 1. for every 3-rd index in the given RNA: - extract the codon at current index - print the codon from previos step

33. Accumulation (count = count + 1) • To keep a running total use the construct: count = count + 1 • This just means: • evaluate the expression on the right side • store the result in the variable on the left side • For example >>>total = 0 >>> total = total + 1 # total is now 1 >>> total = total + 1 # total is now 2 >>> total = total + 1 # total is now 3

34. Accumulation (count = count + 1) • Also works with strings, but it means “append” >>>name = "" >>> name = name + "B" # name is now "B" >>> name = name + "i" # name is now "Bi" >>> name = name + "o" # name is now "Bio" • However, it could mean “prepend” if the order is flipped >>>name = "" >>> name = "B" + name # name is now "B" >>> name = "i" + name # name is now "iB" >>> name = "o" + name # name is now "oiB"

35. Commenting the Code • Comments are programmer’s notes ignored by Python • descriptions of the purpose of functions • annotations of subtle points in the code • annotations of meaning of variables • Comments aid in clarifying your programs to other programmers (and to you after a long break) • Comments can be added via # – anything after # until the end of the line is ignored by Python # computes the average of the given numbers x and y # e.g. average(20, 40) returns 30 defaverage(x, y): result = (x + y) / 2.0 return result