Commit fdc93663 authored by Bertrand  NÉRON's avatar Bertrand NÉRON
Browse files

add code for exercises

parent c92f67f7
......@@ -14,10 +14,16 @@ Exercice
Use the code of the exetrcise 4.5.7 on the kmer. Make a function which compute all kmer of a given lenght
in a sequence.
.. literalinclude:: _static/code/kmer.py
:linenos:
:language: python
:download:`kmer.py <_static/code/kmer.py>` .
Exercise
--------
Write a function translate taht have a nucleic sequence as parameter, and return the translate sequence.
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',
......@@ -43,12 +49,50 @@ bonus
This function have to take the phase as parameter
bonus
"""""
.. literalinclude:: _static/code/translate.py
:linenos:
:language: python
:download:`translate.py <_static/code/translate.py>` .
Exercise
--------
This function can take genetique code as default parameter
Implement a matrix and functions to handle it.
choose the data structure of your choice.
The API (**A**\ pplication **P**\ rogramming **I**\ nterface) to implemet is the following:
.. literalinclude:: _static/code/matrix.py
:linenos:
:language: python
:download:`matrix.py <_static/code/matrix.py>` .
Exercise
--------
Write a program that calculates the similarity of 2 RNA sequences.
* To compute the simalirity you need to parse a file containing the similarity matrix.
* The similarity of the 2 sequences is the sum of base similarities.
so you have to compare the first base of to sequence and use the matrix to get the similarity
from the similarity table, on so on for all bases then sum these similarities.
.. note::
as we don't yet see how to read a file, we provide a list of strings that represents the file
as we can get them if we read that file.
::
lines = iter([' A G C U\n'
'A 1.0 0.5 0.0 0.0\n',
'G 0.5 1.0 0.0 0.0\n',
'C 0.0 0.0 1.0 0.5\n',
'U 0.0 0.0 0.5 1.0\n'])
.. literalinclude:: _static/code/similarity.py
:linenos:
:language: python
:download:`similarity.py <_static/code/similarity.py>` .
\ No newline at end of file
import collections
def kmer(sequence, k):
kmers = collection.defaultdict(int)
for i in range(len(sequence) - k):
kmer = sequence[i:i + k]
kmers[kmer] = kmers.get(kmer, 0) + 1
return kmers
\ No newline at end of file
"""
Implementation of simple matrix
"""
def matrix_maker(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_matrix_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 = matrix_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 matrix_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 matrix_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_matrix_index(matrix, row_no, col_no)
return matrix[col_no][row_no]
def matrix_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_matrix_index(matrix, row_no, col_no)
matrix[col_no][row_no] = val
def matrix_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 matrix_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 matrix_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_matrix_index(matrix, row_no, 0)
row_max, col_max = matrix_size(matrix)
row = []
for col_n in range(col_max):
row.append(matrix_get_cell(matrix, row_no, col_n))
return row
def matrix_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_matrix_index(matrix, row_no, 0)
row_max, col_max = matrix_size(matrix)
for col_n in range(col_max):
matrix_set_cell(matrix, row_no, col_n, val)
def matrix_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_matrix_index(matrix, 0, col_no)
col = matrix[col_no][:]
return col
def matrix_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_matrix_index(matrix, 0, col_no)
row_max, col_max = matrix_size(matrix)
for row_n in range(im):
matrix_set_cell(matrix, row_n, col_no, val)
def matrix_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 = matrix_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_matrix_index(matrix, 0, col_no)
matrix[col_no] = col
def matrix_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 = matrix_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_matrix_index(matrix, row_no, 0)
for col_no, value in enumerate(row):
matrix_set_cell(matrix, row_no, col_no, value)
if __name__ == '__main__':
m = matrix_maker(5, 3)
print m
matrix_set_cell(m,0, 0, 1)
matrix_set_cell(m,0, 2, 2)
matrix_set_cell(m,4, 0, 12)
matrix_set_cell(m,4, 2, 15)
print matrix_to_str(m)
print "get row 0", matrix_get_row(m, 0)
print "get col 0", matrix_get_col(m, 0)
from matrix import *
lines = iter( [' A G C U\n',
'A 1.0 0.5 0.0 0.0\n',
'G 0.5 1.0 0.0 0.0\n',
'C 0.0 0.0 1.0 0.5\n',
'U 0.0 0.0 0.5 1.0\n']
)
def parse_similarity_file():
"""
parse file containing RNA similarity matrix and return a matrix
"""
sim_matrix = matrix_maker(4, 4)
#skip first line
lines.next()
for row_no, line in enumerate(lines):
line = line.strip()
fields = line.split()
values = [float(val) for val in fields[1:]]
matrix_replace_row(sim_matrix, row_no, values)
return sim_matrix
def get_similarity(b1, b2, sim_matrix):
"""
:param b1: the first base must be in ('A', 'G', 'C', 'U')
:type b1: string
:param b2: the first base must be in ('A', 'G', 'C', 'U')
:type b2: string
:param sim_matrix: a similarity matrix
:type sim_matrix: matrix
:return: the similarity between b1 and b2
:rtype: float
"""
bases = {'A':0 , 'G':1, 'C':2, 'U':3}
b1 = b1.upper()
b2 = b2.upper()
if not b1 in bases:
raise KeyError("unknown base b1: " + str(b1))
if not b2 in bases:
raise KeyError("unknown base b2: " + str(b2))
return matrix_get_cell(sim_matrix, bases[b1], bases[b2])
def compute_similarity(seq1, seq2, sim_matrix):
"""
compute a similarity score between 2 RNA sequence of same lenght
:param seq1: first sequence to compare
:type seq1: string
:param seq2: second sequence to compare
:type seq2: string
:param sim_matrix: the similarity between b1 and b2
:type sim_matrix: matrix
:return: the similarity score between seq1 and seq2
:rtype: float
"""
similarities = []
for b1, b2 in zip(seq1, seq2):
sim = get_similarity(b1, b2, sim_matrix)
similarities.append(sim)
return sum(similarities)
if __name__ == '__main__':
seq1 = 'AGCAUCUA'
seq2 = 'ACCGUUCU'
sim_matrix = parse_similarity_file()
print matrix_to_str(sim_matrix)
similarity = compute_similarity(seq1, seq2, sim_matrix)
print similarity
\ No newline at end of file
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 = ''
start = 0
while (start + 2) < len(nuc_seq):
end = start + 3
print start, end
codon = nuc_seq[start:end]
codon = codon.lower()
if codon in code:
prot_seq += code[codon]
else:
raise RuntimeError("unknow codon: " + codon)
start += 3
return prot_seq
def translate2(nuc_seq, code, phase = 1):
prot_seq = ''
if 0 < phase < 4 :
start = phase - 1
elif -4 < phase < 0:
start = -phase - 1
nuc_seq = nuc_seq[::-1]
while(start + 2) < len(nuc_seq):
end = start + 3
codon = nuc_seq[start:end].lower()
if codon in code:
prot_seq += code[codon]
else:
raise RuntimeError("unknow codon")
start += 3
return prot_seq
\ No newline at end of file
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