python 练习26-30题

答案

第二十六题

Introduction to Random Strings

代码块

import  math

with open('D:/py_work/play/file/rosalind_prob.txt') as  f :
    f = f.read().split()

seq = f[0]              #序列
frequency = [float(i) for i in f[1:]]        #C-G对频率

freCG = [j/2 for j in frequency]          #C、G单个碱基的频率
freAT = [(1-i)/2 for i in frequency]      #A、T单个碱基的频率

result = []
j = 0
while j < len(freAT) :            #循环次数
    z = 0
    for i in seq:
        if i == 'C' or i == 'G':
            z += math.log10(freCG[j])
        else:
            z += math.log10(freAT[j])
    result.append(round(z,3))
    j += 1

final = ' '.join(str(i) for i in result)
print(final)

第二十七题

Enumerating Oriented Gene Orderings

代码块

from itertools import permutations ,product

def all_num(n) :
    f = 1
    for i in range(2*n,0,-2):
        f = f * i
    return f

def seq(n) :
    k = []
    item = ((i, -i) for i in range(1, n + 1))          #元组(1，-1)，（2，-2）...
    for p in permutations(item, n):
        # print(p)
        l = [m for m in p]
       # print(l)
        s = list(product(range(2), repeat=n))
        #print(s)
        for i in range(len(s)):
            for j in range(n):
                mm = s[i][j]
                print(p[j][mm], end=' ')

            print('\t')


with open('D:/py_work/play/file/rosalind_sign.txt') as f :
    f = f.read().split()
    f = int(f[0])

    print(all_num(f))
    print(seq(f))

第二十八题

Finding a Spliced Motif

代码块

import re

with open('D:/py_work/play/file/rosalind_sseq.txt') as ds:
    s = ''
    for i in ds:
        s += i.strip()
    str_list = [i for i in re.findall(r'[TACG]+', s)]


begin = 0
for i in range(len(str_list[1])):                       #遍历要找的每个碱基
    for j in range(begin, len(str_list[0])):            #遍历母链
        if str_list[1][i] == str_list[0][j]:
            print(j+1, end=' ')
            begin = j + 1
            break

第二十九题

Transitions and Transversions

代码块

import re

with open('D:/py_work/play/file/rosalind_tran.txt') as  f :
    f = f.read().split()
    s = ''
    for i in f :
        s += i
        x = re.findall(r'[ATCG]+',s)

def tra(x):             #转换
    x_2 = ''
    for i in x :
        if i == 'A' :
            i = 'G'
        elif i == 'C' :
            i = 'T'
        elif i == 'G' :
            i = 'A'
        elif i == 'T' :
            i = 'C'
        x_2 += i
    return x_2

y = tra(x[1])
l = len(x[0])
num = 0
mi = 0
for j in range(l) :
    if x[0][j] == y[j] :            #转换
        num += 1
    elif x[0][j] == x[1][j] :       #颠换
        mi += 1
mis = l - mi -num

print((num/mis))

第三十题

k-Mer Composition

代码块

import  re

def fuction(n) :                                                    #制作key值
    jianji = ['A','C','G','T']
    result = []
    for i in jianji :
        for j in jianji :
            for x in jianji :
                for y in jianji :
                    result.append(''.join(i+j+x+y))
    return result

with open('D:/py_work/play/file/rosalind_kmer.txt') as f :
    l = []
    s = ''
    for i in f :
        s += i.rstrip()
        l = [re.findall(r'[ACGT]+',s)][0]

length = l[0]
#4个相邻碱基为一组k-mer
def consume(length) :
    result = [0] * 4 ** 4                                                   #k=4时的碱基表，例【AAAA,AAAC,AAAG,AAAT,AACA,AAGA,......,TTTT】
    dict_1 = dict(zip(list(fuction(1)), list(range(4 ** 4))))               # 做字典
    i = 0
    while i <= len(length) - 4 :                    
        k_mer = length[i:i +4]
        index = dict_1[k_mer]
        result[index] += 1
        i += 1
    return result

result = consume(length)
export = ' '.join(str(i) for i in result)
print(export)

https://rosalind.info/problems/
https://www.bilibili.com/read/readlist/rl58094?spm_id_from=333.999.0.0
https://www.zhihu.com/people/shan-shang-fa-shen-jing-93/posts