.. sectnum:: :start: 7 .. _Control_Flow_Statements: *********************** Control Flow Statements *********************** Exercises ========= Exercise -------- The Fibonacci sequence are the numbers in the following integer sequence: 0, 1, 1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144, ... By definition, the first two numbers in the Fibonacci sequence are 0 and 1, and each subsequent number is the sum of the previous two. The fibonacci suite can be defined as following: | F\ :sub:`0` = 0, F\ :sub:`1` = 1. | | F\ :sub:`n` = F\ :sub:`n-1` + F\ :sub:`n-2` Write a function which take an integer ``n`` as parameter and returns a list containing the ``n`` first number of the Fibonacci sequence. .. literalinclude:: _static/code/fibonacci_iteration.py :linenos: :language: python :download:`fibonacci_iteration.py <_static/code/fibonacci_iteration.py>` . We will see another way more elegant to implement the fibonacci suite in :ref:`Advanced Programming Techniques` section. Exercise -------- Reimplement your own function max (my_max). This function will take a list or tuple of float or integer and returns the largest element? Write the pseudocode before to propose an implementation. pseudocode ^^^^^^^^^^ | *function my_max(l)* | *max <- first elt of l* | *for each elts of l* | *if elt is > max* | *max <- elt* | *return max* implementation ^^^^^^^^^^^^^^ :: def my_max(seq): """ return the maximum value in a sequence work only with integer or float """ higest = seq[0] for i in seq: if i > highest: highest = i return highest l = [1,2,3,4,58,9] print(my_max(l)) 58 .. _enzyme_exercise: Exercise -------- | We want to establish a restriction map of a sequence. | But we will do this step by step. | and reuse the enzymes used in previous chapter: * create a function that take a sequence and an enzyme as parameter and return the position of first binding sites. (write the pseudocode) **pseudocode** | *function one_enz_binding_site(dna, enzyme)* | *if enzyme binding site is substring of dna* | *return of first position of substring in dna* **implementation** .. literalinclude:: _static/code/restriction.py :linenos: :lines: 1-13 :language: python * improve the previous function to return all positions of binding sites **pseudocode of first algorithm** | *function one_enz_binding_sites(dna, enzyme)* | *positions <- empty* | *if enzyme binding site is substring of dna* | *add the position of the first substring in dna in positions* | *positions <- find binding_sites in rest of dna sequence* | *return positions* **implementation** .. literalinclude:: _static/code/restriction.py :linenos: :lines: 13-25 :language: python **pseudocode of second algorithm** | *function one_enz_binding_sites(dna, enzyme)* | *positions <- empty* | *find first position of binding site in dna* | *while we find binding site in dna* | *add position of binding site to positions* | *find first position of binding site in dna in rest of dna* | *return positions* **implementation** .. literalinclude:: _static/code/restriction.py :linenos: :lines: 25-36 :language: python search all positions of Ecor1 binding sites in dna_1 :: import collections RestrictEnzyme = collections.namedtuple("RestrictEnzyme", "name comment sequence cut end") ecor1 = RestrictEnzyme("EcoRI", "Ecoli restriction enzime I", "gaattc", 1, "sticky") dna_1 = """tcgcgcaacgtcgcctacatctcaagattcagcgccgagatccccgggggttgagcgatccccgtcagttggcgtgaattcag cagcagcgcaccccgggcgtagaattccagttgcagataatagctgatttagttaacttggatcacagaagcttccaga ccaccgtatggatcccaacgcactgttacggatccaattcgtacgtttggggtgatttgattcccgctgcctgccagg""" * generalize the binding sites function to take a list of enzymes and return a list of tuple (enzyme name, position) **pseudocode** | *function binding_sites(dna, set of enzymes)* | *positions <- empty* | *for each enzyme in enzymes* | *pos <- one_enz_binding_sites(dna, enzyme)* | *pos <- for each position create a tuple enzyme name, position* | *positions <- pos* | *return positions* **implementation** in bonus we can try to sort the list in the order of the position of the binding sites like this: [('Sau3aI', 38), ('SmaI', 42), ('Sau3aI', 56), ('EcoRI', 75), ... .. literalinclude:: _static/code/restriction.py :linenos: :lines: 37- :language: python :: import collections RestrictEnzyme = collections.namedtuple("RestrictEnzyme", ("name", "comment", "sequence", "cut", "end") ecor1 = RestrictEnzyme("EcoRI", "Ecoli restriction enzime I", "gaattc", 1, "sticky") ecor5 = RestrictEnzyme("EcoRV", "Ecoli restriction enzime V", "gatatc", 3, "blunt") bamh1 = RestrictEnzyme("BamHI", "type II restriction endonuclease from Bacillus amyloliquefaciens ", "ggatcc", 1, "sticky") hind3 = RestrictEnzyme("HindIII", "type II site-specific nuclease from Haemophilus influenzae", "aagctt", 1 , "sticky") taq1 = RestrictEnzyme("TaqI", "Thermus aquaticus", "tcga", 1 , "sticky") not1 = RestrictEnzyme("NotI", "Nocardia otitidis", "gcggccgc", 2 , "sticky") sau3a1 = RestrictEnzyme("Sau3aI", "Staphylococcus aureus", "gatc", 0 , "sticky") hae3 = RestrictEnzyme("HaeIII", "Haemophilus aegyptius", "ggcc", 2 , "blunt") sma1 = RestrictEnzyme("SmaI", "Serratia marcescens", "cccggg", 3 , "blunt") and the 2 dna fragments: :: dna_1 = """tcgcgcaacgtcgcctacatctcaagattcagcgccgagatccccgggggttgagcgatccccgtcagttggcgtgaattcag cagcagcgcaccccgggcgtagaattccagttgcagataatagctgatttagttaacttggatcacagaagcttccaga ccaccgtatggatcccaacgcactgttacggatccaattcgtacgtttggggtgatttgattcccgctgcctgccagg""" dna_2 = """gagcatgagcggaattctgcatagcgcaagaatgcggccgcttagagcgatgctgccctaaactctatgcagcgggcgtgagg attcagtggcttcagaattcctcccgggagaagctgaatagtgaaacgattgaggtgttgtggtgaaccgagtaag agcagcttaaatcggagagaattccatttactggccagggtaagagttttggtaaatatatagtgatatctggcttg""" enzymes= (ecor1, ecor5, bamh1, hind3, taq1, not1, sau3a1, hae3, sma1) binding_sites(dna_1, enzymes) [('Sau3aI', 38), ('SmaI', 42), ('Sau3aI', 56), ('EcoRI', 75), ('SmaI', 95), ('EcoRI', 105), ('Sau3aI', 144), ('HindIII', 152), ('BamHI', 173), ('Sau3aI', 174), ('BamHI', 193), ('Sau3aI', 194)] binding_sites(dna_2, enzymes) [('EcoRI', 11), ('NotI', 33), ('HaeIII', 35), ('EcoRI', 98), ('SmaI', 106), ('EcoRI', 179), ('HaeIII', 193), ('EcoRV', 225)] :download:`restriction.py <_static/code/restriction.py>` . Exercise -------- From a list return a new list without any duplicate, but keeping the order of items. For example: :: >>> l = [5,2,3,2,2,3,5,1] >>> uniqify_with_order(l) >>> [5,2,3,1] solution :: >>> uniq = [] >>> for item in l: >>> if item not in uniq: >>> uniq.append(item) solution :: >>> uniq_items = set() >>> l_uniq = [x for x in l if x not in uniq_items and not uniq_items.add(x)]