8   Dive into Functions¶

8.1   Exercises¶

8.1.1   Exercise¶

Without executing the code in Python interpreter, can you determine what the code below print out. help you by drawing diagram.

Hint locals print a dictionary with local variable as keys and their respective values.

x = 4

def func():
y  = 5
print locals()

>>> func()
{'y': 5}
>>> print x
4


8.1.2   Exercise¶

Without executing the code in Python interpreter, can you determine what the code below print out. help you by drawing diagram.

Hint locals print a dictionary with local variable as keys and their respective values.

x = 4

def func():
y = 5
x = 8
print locals()
x = x + 2

>>> y = func()
{'y': 5, 'x': 8}
>>>
>>> print y
None
>>> print x
4


8.1.3   Exercise¶

Without executing the code in Python interpreter, can you determine what the code below print out. help you by drawing diagram.

Hint locals print a dictionary with local variable as keys and their respective values.

x = 4

def func(a):
y = x + 2
print locals()
x = y
return y

>>> y = func(x)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "<stdin>", line 2, in func
UnboundLocalError: local variable 'x' referenced before assignment


Unlike what we might think in y = x + 2 x is not get from the global scope. As soon as you make an assignment to a variable in a scope, that variable becomes local to that scope and shadows any similarly named variable in the outer scope. even if the assignment appear later in code. Here x = y make x as local variable whatever you are in func. so at line y = x + 2 we try to use the local variable x but we have to asign it a value (it is done later) so Python raise an UnboundLocalError (see python faq for details)

8.1.4   Exercise¶

Without executing the code in Python interpreter, can you determine what the code below print out. help you by drawing diagram.

Hint locals print a dictionary with local variable as keys and their respective values.

x = 4

def func(a):
x = x + 2
print locals()
return x

y = func(x)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "<stdin>", line 2, in func
UnboundLocalError: local variable 'x' referenced before assignment

print y
print y == x


8.1.5   Exercice¶

Without executing the code in Python interpreter, can you determine what the code below print out. help you by drawing diagram.

x = 4

def func(x):
x = x + 2
return x

y = func(x)

>>> print x
4
>>> print y == x
False


8.1.6   Exercice¶

Without executing the code in Python interpreter, can you determine what the code below print out. help you by drawing diagram.

def func():
y = x
return y

>>> x = 4
>>> z = func()
>>>
>>> print x
4
>>> print z
4
>>> print id(z) == id(x)
True


8.1.7   Exercice¶

Without executing the code in Python interpreter, can you determine what the code below print out. help you by drawing diagram.

x = 4

def func(x = 5):
x = x + 2
return x

>>> y = func(x)
>>>
>>> print x
4
>>> print y
6


8.1.8   Exercice¶

Without executing the code in Python interpreter, can you determine what the code below print out. help you by drawing diagram.

Hint locals print a dictionary with local variable as keys and their respective values.

x = 4

def func(a):
global x
def func2():
print locals()
y = x + 4
return y
z = func2()
return z

y = func(x)
{}
>>> print x
4
>>> print y
8


8.1.9   Exercice¶

Without executing the code in Python interpreter, can you determine what the code below print out. help you by drawing diagram.

x = {'a' : 4}

def func(a):
a['b'] = 5
return a

y = func(x)

>>> print x
{'a': 4, 'b': 5}
>>> print y
{'a': 4, 'b': 5}
>>> print x is y
True


8.1.10   Exercice¶

Without executing the code in Python interpreter, can you determine what the code below print out. help you by drawing diagram.

x = {'a' : 4}

def func(a):
a['b'] = 5

y = func(x)

>>> print x
{'a': 4, 'b': 5}
>>> print y
None


8.1.11   Exercice¶

Without executing the code in Python interpreter, can you determine what the code below print out. help you by drawing diagram.

x = {'a' : 4}

def func(a):
x['b'] = 5
def func2():
a['b'] = 6
return a

y = func(x)

print x
{'a': 4, 'b': 5}
print y
{'a': 4, 'b': 5}

a refer to same object as x
in func x does not exist, so x refer to global variable x
we mutate x
func2 is never executed
we return a so the same object referred by x
so y refer also the same object as x

8.1.12   Exercice¶

Without executing the code in Python interpreter, can you determine what the code below print out. help you by drawing diagram.

x = {'a' : 4}

def func(a):
x['b'] = 5
def func2():
a['b'] = 6
func2()
return a

y = func(x)

print x
{'a': 4, 'b': 6}

in this code func2 is executed
a is not in func2 namespace so python find it in enclosing namespace func
a refer the same object as x

8.1.13   Exercice¶

Without executing the code in Python interpreter, can you determine what the code below print out. help you by drawing diagram.

x = {'a' : 4}

def func(a):
x['b'] = 5
def func2(x):
x['b'] = 6
func2(a.copy())
return a

y = func(x)

print x
{'a': 4, 'b': 5}

in this code x a variable x is defined locally in func2 and hide the global variable x
this local x refer to a shallow copy of the func local variable a which refer to the same object as global variable x
so func2 does not do a side effect on dictionary referred by x as in previous example.

8.1.14   Exercice¶

Use the code of the exercise 4.5.7 on the kmer. Make a function which compute all kmer of a given length in a sequence.

  1 2 3 4 5 6 7 8 9 10 11 12  def get_kmer_occurences(seq, kmer_len): """ return a list of tuple each tuple contains a kmers present in seq and its occurence """ kmers = {} stop = len(seq) - kmer_len for i in range(stop + 1): kmer = s[i : i + kmer_len] kmers[kmer] = kmers.get(kmer, 0) + 1 return kmers.items() 

8.1.15   Exercise¶

Write a function translate that have a nucleic sequence as parameter, and return the translate sequence. We give you a genetic code :

code = {  'ttt': 'F', 'tct': 'S', 'tat': 'Y', 'tgt': 'C',
'ttc': 'F', 'tcc': 'S', 'tac': 'Y', 'tgc': 'C',
'tta': 'L', 'tca': 'S', 'taa': '*', 'tga': '*',
'ttg': 'L', 'tcg': 'S', 'tag': '*', 'tgg': 'W',
'ctt': 'L', 'cct': 'P', 'cat': 'H', 'cgt': 'R',
'ctc': 'L', 'ccc': 'P', 'cac': 'H', 'cgc': 'R',
'cta': 'L', 'cca': 'P', 'caa': 'Q', 'cga': 'R',
'ctg': 'L', 'ccg': 'P', 'cag': 'Q', 'cgg': 'R',
'att': 'I', 'act': 'T', 'aat': 'N', 'agt': 'S',
'atc': 'I', 'acc': 'T', 'aac': 'N', 'agc': 'S',
'ata': 'I', 'aca': 'T', 'aaa': 'K', 'aga': 'R',
'atg': 'M', 'acg': 'T', 'aag': 'K', 'agg': 'R',
'gtt': 'V', 'gct': 'A', 'gat': 'D', 'ggt': 'G',
'gtc': 'V', 'gcc': 'A', 'gac': 'D', 'ggc': 'G',
'gta': 'V', 'gca': 'A', 'gaa': 'E', 'gga': 'G',
'gtg': 'V', 'gcg': 'A', 'gag': 'E', 'ggg': 'G'
}


8.1.15.1   bonus¶

This function have to take the phase as parameter

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 genetic_code = { 'ttt': 'F', 'tct': 'S', 'tat': 'Y', 'tgt': 'C', 'ttc': 'F', 'tcc': 'S', 'tac': 'Y', 'tgc': 'C', 'tta': 'L', 'tca': 'S', 'taa': '*', 'tga': '*', 'ttg': 'L', 'tcg': 'S', 'tag': '*', 'tgg': 'W', 'ctt': 'L', 'cct': 'P', 'cat': 'H', 'cgt': 'R', 'ctc': 'L', 'ccc': 'P', 'cac': 'H', 'cgc': 'R', 'cta': 'L', 'cca': 'P', 'caa': 'Q', 'cga': 'R', 'ctg': 'L', 'ccg': 'P', 'cag': 'Q', 'cgg': 'R', 'att': 'I', 'act': 'T', 'aat': 'N', 'agt': 'S', 'atc': 'I', 'acc': 'T', 'aac': 'N', 'agc': 'S', 'ata': 'I', 'aca': 'T', 'aaa': 'K', 'aga': 'R', 'atg': 'M', 'acg': 'T', 'aag': 'K', 'agg': 'R', 'gtt': 'V', 'gct': 'A', 'gat': 'D', 'ggt': 'G', 'gtc': 'V', 'gcc': 'A', 'gac': 'D', 'ggc': 'G', 'gta': 'V', 'gca': 'A', 'gaa': 'E', 'gga': 'G', 'gtg': 'V', 'gcg': 'A', 'gag': 'E', 'ggg': 'G' } def translate(nuc_seq, code): prot_seq = '' n = 0 # to avoid to compute len(seq)/3 at each loop # I compute it once and use a reference # it could be expensive if the sequence is very long. # another way to determine the end of looping # stop_iteration = len(nuc_seq) # while (start + 2) < stop_iteration: cycle = len(nuc_seq)//3 while n < cycle: start = n * 3 end = start + 3 codon = nuc_seq[start:end] codon = codon.lower() if codon in code: prot_seq += code[codon] else: raise RuntimeError("unknow codon: " + codon) n += 1 # if use the other looping solution # n += 3 return prot_seq def translate2(nuc_seq, code, phase = 1): prot_seq = '' if 0 < phase < 4 : start = phase - 1 nuc_seq = nuc_seq[start:] elif -4 < phase < 0: start = -phase - 1 nuc_seq = nuc_seq[::-1] nuc_seq = nuc_seq[start:] prot_seq = translate(nuc_seq, code) return prot_seq 

8.1.16   Exercise¶

Write a program that calculates the similarity of 2 RNA sequences.

• To compute the similarity you need to parse a file containing the similarity matrix.

Hint: use the module containing the functions that handle a matrix from previous chapter. put this matrix.py file in a directory named “my_python_lib” in your home or Desktop and import it in your current program (the similarity script must be placed elsewhere).

• The similarity of the 2 sequences is the sum of base similarities. so you have to compare the first base of two sequences and use the matrix to get the similarity from the similarity table, on so on for all bases then sum these similarities.

First implementation

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 """ Implementation of simple matrix """ def create(row_num, col_num, val=None): """ :param row_num: the number of rows :type row_num: int :param col_num: the number of columns :type col_num: int :param val: the default value to fill the matrix :type val: any (None by default) :return: matrix of rows_num x col_num :rtype: matrix """ matrix = [] for i in range(col_num): col = [val] * row_num matrix.append(col) return matrix def _check_index(matrix, row_no, col_no): """ check if row_no and col_no are in matrix bound :param matrix: the matrix to compute the size :type matrix: matrix :param rows_no: the index of row to check :type rows_no: int :param col_no: the index of column to check :type col_no: int :raise: IndexError if row_no or col_no are out of matrix bounds """ row_max, col_max = size(matrix) if (row_no < 0 or row_no >= row_max) or (col_no < 0 or col_no >= col_max): raise IndexError("matrix index out of range") def size(matrix): """ :param matrix: the matrix to compute the size :type matrix: matrix :return: the size of matrix (number of rows, number of cols) :rtype: typle of 2 int """ return len(matrix[0]), len(matrix) def get_cell(matrix, row_no, col_no): """ :param matrix: the matrix :type matrix: matrix :param rows_no: the row number :type rows_no: int :param col_no: the column number :type col_no: int :retrun: the content of cell corresponding to row_no x col_no :rtype: any """ _check_index(matrix, row_no, col_no) return matrix[col_no][row_no] def set_cell(matrix, row_no, col_no, val): """ set the value val in cell specified by row_no x col_no :param matrix: the matrix to modify :type matrix: matrix :param row_no: the row number of cell to set :type rows_no: int :param col_no: the column number of cell to set :type col_no: int :param val: the value to set in cell :type val: int """ _check_index(matrix, row_no, col_no) matrix[col_no][row_no] = val def to_str(matrix): """ :param matrix: the matrix to compute the size :type matrix: matrix :return: a string representation of the matrix :rtype: str """ s = "" # by design all matrix cols have same size for row in zip(*matrix): cells = [str(cell) for cell in row] s += " ".join(cells) + "\n" return s def mult(matrix, val): """ :param matrix: the matrix to compute the size :type matrix: matrix :param rows_no: the number of rows :type rows_no: int :param col_no: the number of columns :type col_no: int :param val: the value to mult the matrix with :type val: int :return: a new matrix corresponding the scalar product of matrix * val :rtype: matrix """ new_matrix = [] for col in matrix: new_col = [cell * val for cell in col] new_matrix.append(new_col) return new_matrix def get_row(matrix, row_no): """ :param matrix: the matrix to compute the size :type matrix: matrix :param rows_no: row number :type rows_no: int :return: the row of matrix corresponding to row_no a shallow copy of the row :rtype: list """ _check_index(matrix, row_no, 0) row_max, col_max = size(matrix) row = [] for col_n in range(col_max): row.append(get_cell(matrix, row_no, col_n)) return row def set_row(matrix, row_no, val): """ set all cells of row row_no with val :param matrix: the matrix to modify :type matrix: matrix :param row_no: the row number :type row_no: int :param val: the value to put in cells :type val: any """ _check_index(matrix, row_no, 0) row_max, col_max = size(matrix) for col_n in range(col_max): set_cell(matrix, row_no, col_n, val) def get_col(matrix, col_no): """ :param matrix: the matrix get row :type matrix: matrix :param col_no: the column number :type col_no: int :return: the column corresponding to col_no of matrix a shallow copy of the col :rtype: list """ _check_index(matrix, 0, col_no) col = matrix[col_no][:] return col def set_col(matrix, col_no, val): """ set all cells of col col_no with val :param matrix: the matrix to compute the size :type matrix: matrix :param col_no: the column number :type col_no: int :param val: the value to put in cells :type val: any """ _check_index(matrix, 0, col_no) for row_n in range(matrix): set_cell(matrix, row_n, col_no, val) def replace_col(matrix, col_no, col): """ replace column col_no with col :param matrix: the matrix to compute the size :type matrix: matrix :param col_no: the column number to replace :type col_no: int :param col: the list of values to use as replacement of column :type col: list """ row_max, col_max = size(matrix) if len(col) != col_max: raise RuntimeError("the size of col {0} does not fit to matrix size {1}x{2}".format(len(col), row_max, col_max)) _check_index(matrix, 0, col_no) matrix[col_no] = col def replace_row(matrix, row_no, row): """ replace row row_no with row :param matrix: the matrix to compute the size :type matrix: matrix :param row_no: the column number :type row_no: int :param row: the list of value to use as replacement of row :type row: list """ row_max, col_max = size(matrix) if len(row) != row_max: raise RuntimeError("the size of row {0} does not fit to matrix size {1}x{2}".format(len(row), row_max, col_max)) _check_index(matrix, row_no, 0) for col_no, value in enumerate(row): set_cell(matrix, row_no, col_no, value) if __name__ == '__main__': m = create(5, 3) print(m) set_cell(m, 0, 0, 1) set_cell(m, 0, 2, 2) set_cell(m, 4, 0, 12) set_cell(m, 4, 2, 15) print(to_str(m)) print("get row 0", get_row(m, 0)) print("get col 0", get_col(m, 0)) 

Second implementation

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 # matrix is implemented by list of list def matrix_maker(ligne, col, val=None): m = [] for i in range(ligne): c = [val]*col m.append(c) return m #---- functions that depends on the matrix srtructure def matrix_size(m): return len(m), len(m[0]) def matrix_get(matrix, i, j): _check_matindex(matrix,i,j) return matrix[i][j] def matrix_set(matrix, i, j, val): _check_matindex(matrix,i,j) matrix[i][j] = val def matrix_print(m): im, jm = matrix_size(m) for i in range(im): print m[i] #---- independant regarding matrix structure def _check_matindex(matrix,i,j): imax, jmax = matrix_size(matrix) if (i < 0 or i >= imax) or (j < 0 or j>= jmax): raise IndexError, "matrix index out of range" def matrix_get_line(matrix, i): _check_matindex(matrix,i,0) im, jm = matrix_size(matrix) line = [] for n in range(jm): line.append(matrix_get(matrix, i, n)) return line def matrix_set_line(matrix, i, val): _check_matindex(matrix,i,0) im, jm = matrix_size(matrix) for n in range(jm): matrix_set(matrix, i, n, val) def matrix_get_col(matrix, j): _check_matindex(matrix,0,j) im, jm = matrix_size(matrix) col = [] for n in range(im): col.append(matrix_get(matrix, n, j)) return col def matrix_set_col(matrix, j, val): _check_matindex(matrix,0,j) im, jm = matrix_size(matrix) for n in range(im): matrix_set(matrix, n, j, val) if __name__ == '__main__': m = matrix_maker(5, 3) matrix_set(m,0, 0, 1) matrix_set(m,0, 2, 2) matrix_set(m,4, 0, 12) matrix_set(m,4, 2, 15) matrix_print(m) print "get line 0", matrix_get_line(m, 0) print "get col 0", matrix_get_col(m, 0)