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# Introduction: # * Who are we # * Organisation of the first week # * Group work in the second week # * Quick overview of projects # * Organisation of the second week # * How will we rate? # * Questions? # Python is a scripting language -> exactly the commands you enter are executed by the interpreter # Exception: Everything after a # is a comment, the interpreter ignores it # Simplest use: claculator # Run the following command: 2+2 # Whitespace within a command doesn't matter: 30 - 7+2 # Try to stick to one style though # Whitespace before a command does though, we'll come to that later: 30 - 7 + 2 # The usual rules of arithmetics apply: 50 - 5 * 6 5 + 4 / 2 #There are a few additional useful operators: 17 / 3 # classic division returns a float 17 // 3 # floor division discards the fractional part 17 % 3 # the % operator returns the remainder of the division 5 * 3 + 2 # result * divisor + remainder 5 ** 2 # x ** y is x to the yth power # You can define variables and give them values using the = sign, the names have to start with a # letter or an underscore and can contain letters, numbers and underscoes: N0 = 200 # Number of bacteria in the parental generation Q = 2 # Number of offspring per generation n = 10 # Number of generations # Now we can calculate the number of bacteria in generation n: N0 * Q ** n # Note that we can use only variables that have been defined previously: N0 * Q2 ** n Q2 = 4 N0 * Q2 ** n # And that there is a difference between lower- and higher-case letters N0 * q2 ** n # We can also assign the result directly to a new variable: Nn = N0 * Q ** n # Note how, when we assign something to a variable, it isn't printed on the console any more. # To print something to the console, we can use the function print: print(Nn) # print is a function: It is a piece of reusable code that does something to the arguments passed to it. # The general structure is: function(argument_1, argument_2, ... argument_n). There are many useful # built-in functions and many more in modules - collections of functions provided by the Python developers # or the community - that Andy, Simon and Alona are going to talk about. # For now, this is how you can define and run your own function: def plus(value_1, value_2): # function name: plus, two arguments: value_1 and value_2 result = value_1 + value_2 return result plus(3, 12) # There two new concepts in the lines above: Blocks and Statements. Let's start with blocks: # Every time a line ends with a colon, what follows is called a block. A block can be recognised # by consistent indentation and ends with the first non-indented line. The colon means that the # line ending with it relates to the entire block following it. So the line: # def plus(value_1, value_2): defines a new funtion made from the block below, which ends with # return result - because the next line, plus(3, 12), is not indented anymore. # A statement is like a function but without the brackets. You cannot define your own statements, # they are integral parts of the language. This is just a side note and not something that is likely # to be relevant to you, just note that "return" is a statement, not a function. # Exercises: # * Write a function calc_offspring(N0, Q, n) that calculates the number of bacteria in generation # n given Q and N0 using the above formula. # * Write a function calc_coli_offspring(n) that calculates the number of coli bacteria after n # generations given that there is just one bacterium to start with and each bacterium generates # exactly 2 offspring per generation # * Modify the two above functions to print the result in addition to returning it # There are different types of variables in Python. We are going to look at many over the course # of this week, but let's start with the two most common ones: floats and strings. # Every number you are likely to encounter is a float (or an integer, but Python 3+ takes care of # necessary conversions automatically). Text is stored in strings that are defined as text between # quotes: text = "Something" print(text) # When you want to use a string, you have to use the quotes, otherwise Python will think you mean a # variable - this is an extremely common mistake: text = Something # If something is a text, Python can not understand its contents - the following does not work: text = "12" 5 + text # You first have to convert the text to a number (float or integer) using the appropriate function: # float and int are functions that take a string as an argument and return a float or an integer number = float(text) 5 + number # or: 5 + float(text) # You can also add strings together: part_1 = "There are " part_2 = " students in this room." print(part_1 + part_2) # However, as we have seen before, we can't add strings and numbers: num_students = 14 print(part_1 + num_students + part_2) # We first have to convert the number to a string: print(part_1 + str(num_students) + part_2) # The character \ is special in strings, it makes the next character special: # \": The quote will be part of the string instead of ending the string print("He said: \"I don't think so\".") # \n: This is a newline print("This text\nconsists of\nseveral lines.") # \\: This is just the character \ print("Otherwise, how would you print \\n instead of inserting a newline?") # Exercises: # * Write a function get_num_copies(cT, E, num_cT) that calculates the number of copies of a template in a # PCR reaction given the cT value, the efficiency of the reaction (how many new molecules are created # from the a molecule of template in one round of amplification) and the number of molecules necessary to # create the threshold signal intensity. Have this function print the following result: # "There were <number> molecules in the mix if the cT was reached after <number> cycles at an efficiency of <number>" # * Extend the functions from the first exercise to also print pretty reports of their results # Now let's come to a more interesting data type: Arrays. # Instead of holding a single value, an array holds several of them - think of them as vectors: data = [1,3,5,7,9,33,12,7] print(data) # You can access single values in an array using a so-called index, with the first value having the # index 0: data[0] data[3] # The number of elements in an array can be found using the function len: len(data) # Remember that we start counting from 0, so the last element in an array is the number of elements - 1 data[len(data)] # This does not work, as the index len(data) points to an element that is not in the array data[len(data) - 1] # You can also access the last elements by counting from behind: data[-1] data[-2] # Arrays can also be "sliced" - you can create a sub-array containing a range of elements: data[2:5] # 3 elements from the range [2,5): including data[2] but excluding data[5] # You can also slice from the start or until the end by omitting the first or last index: data[:3] data[3:] # Slicing can be used to replace or remove elements: data[3:5] = [1,1,1,1] data[4:6] = [] # Arrays can also be concatenated: dat_1 = [1,2,3] dat_2 = [4,5,6] dat_both = dat_1 + dat_2 dat_both += [7] # "x += y" means "x = x + y", this also works for -=, /= and *= # And the cool thing? Strings understand all of these array operations, since a string is more or less # just an array of letters! text = "This is a sentence." text[0] text[:4] text[-1] # The one thing that does not work is replacing elements: text[5:7] = "was" # But strings can be added together: text = "This" text += " is " text += " a horrible " text += " example." # This is indeed a horrible example - this operation is insanely slow and should only be done for # very small datasets. In the next days you will learn a more computationally efficient way of adding # strings together, but for now, let's just go with this. # Of course, we can do more complex things than just add numbers and text together. For that, we\ # need control structures, such as loops: a = 0 while a < 10: print(a) a += 1 # The structure of this loop is: while condition is met, do something. Here again we have a colon followed # by a block: The block of code after the loop is executed again and again until the condition is not # met any more. Remember that this could be forever: a = 0 b = 0 while a < 10: print("a: " + str(a) + ", b: " + str(b)) b += 1 # The infinite loop is a very common problem and not always as easy to find as in the example above. # One use of the while loop is to iterate over an array: data = [1,5,7,3,2] i = 0 while i < len(data): print("Element " + str(i) + ": " + str(data[i])) i += 1 # There is also another kind of loop that can be used when the exact position within the array is not # interesting and that greatly reduces the risk of creating an infinite loop: for x in data: print(x) # In the for loop, a running variable is defined (x) and an array is provided (data). For each element # in the array, the loop block is executed once with x having the value of the element. # A useful function that is often used in connection with the for loop is the range function - it # generates a list of numbers in a certain range: for i in range(5): print(i) # Range has up to three arguments: from, to and step: for i in range(5, 10): print(i) for i in range(0,10,3): print(i) # By the way: range and len together can be used to substitute the while loop in some cases: data = [1,5,7,3,2] for i in range(len(data)): print("Element " + str(i) + ": " + str(data[i])) # Exercises (don't use the equivalent built-in functions): # * Write a function my_sum(values) that takes an array and calculates the sum of the values in the array # * Write a function my_mean(values) that takes an array and calculates the mean of the values in the array # * Write a function my_fac(val) that calculates the factorial of a value (e.g. 5! = 1*2*3*4*5 = 120) # * Write a function my_fib(val) that prints (or returns) the fibonacci series of the length val. # The fibonacci series is a series of numbers that starts with [0, 1]. It is continued by adding the # last two numbers of the series - so my_fib(8) would be # 0, 1, 1 (0+1), 2 (1+1), 3 (1+2), 5 (2+3), 8 (3+5), 13 (5+8) # You will likely need to use more than one variable. # In order to write really meaningful code, there is one more control statement that we need to look at: if x = 5 if x < 10: print("X is less than 10") # This works for both numbers and strings: world = "round" if world == "flat": print("Don't fall off!") # Note the use of "==" here - "=" is used to assign a value, "==" is used to test for equality. # Conceptionally, this is really simple - if a condition is met, execute the block afterwards. # If can also be extended using one or more elif - do something if none of the conditions above was # satisfied and this conditions is - and, if needed, a final else - do something if none of the # conditions above was satisfied. x = 15 if x < 10: print("X is less than 10") elif x < 20: print("X is between 10 and 20") else: print("X is 20 or more") # The conditions can be arbitrarily complex and use any previously defined or built-in functions: data = [1,5,7,3,2] if max(data) < 8: print("There are no values larger than 7 in the data array") # They can also be combined using the keywords "and" and "or": if max(data) < 6 or max(data) > 8: print("The maximum value in the array is between 6 and 8") elif max(data) == 7 and data[0] == 1: print("The maximum value of the array is 7 and its first value is 0") # Though conceptionally simple, this is what gives you immense power in programming - choosing # what to do when is the most important question. # It is important to note that blocks of code can be nested: You can use if in a loop: for x in range(0, 10): if x > 5 and x < 8: print(x) else: print("waiting...") # And vice versa: data = [1,2,3,4,5,6,7,8,9,10] printed = 0 if len(data) < 10: for x in data: print(x) printed += 1 else: print("Data too long, only using the first 5 elements.") for x in data[:5]: print(x) printed += 1 print("Processed " + str(printed) + "values.") # Exercises: # * Write a function my_abs(value) that returns the absolute value of value (e.g. my_abs(-3) = 3) # * Write a function maxdiff(array) that takes an array and returns the largest difference between two # consecutive numbers in the array. So the result for maxdiff([1,2,4,12,7]) would be 8 (|4-12|) # * Write a function count_a(seq) that, given a sequence, counts the number of As. So the result for # count_a("AGTCTGGCATGGCTA") would be 3. # * Extend the function above to count_base(seq, base) that, given a sequence, counts the number of # occurrences of base. So the result for count_base("ACGTCGCTAGC", "C") would be 4. # * Write a function rev(seq) that returns a reversed sequence. So the result for rev("AGGTC") would # be "CTGGA" # * Write a function compl(seq) that returns a complemented sequence. So the result for compl("CTGGA") # would be "GACCT" # * Using the two above functions (don't overwrite them or copy the code, call them!) write a function # reverse_complement(seq) that returns the reverse complement of the sequence seq. # * Write a function find_codon(seq, frame, codon) that, given a sequence, a translation frame (0, 1 or 2) # and a codon either returns the AA position of the codon in the sequence or -1 if it was not found. So # the result for find_codon("AGGTGTAGCA", 0, "TAG") should be -1 and the result for # find_codon("AGGTGTAGCA", 2, "TAG") should be 2 (the second amino acid from the start of the sequence # given the frame) # * Using the first function from the exercise (don't overwrite it, call it from your new function), write # a function count_bases(seq) that prints a table of the frequencies of bases in the sequence. # Be creative, the result for count_bases("AAGTATCC") could be something like" # Base Occurrence Frequency # A 3 37.5% # G 1 12.5% # T 2 25% # C 2 25% # For bonus points, deal with unsanitary input ("AAGTATCC" could also be "AAG TAT CC") - can you # get that to work correctly? # * Write a function maxanydiff(array) that, given an input array, finds the maximum difference between # any two values in the array. So the result for maxanydiff([1,2,4,12,7]) would be 11 (12-1).