# Problem
# A matrix is a rectangular table of values divided into rows and columns. An m×n matrix has m rows and n columns. Given a matrix A, we write Ai,j to indicate the value found at the intersection of row i and column j.
# Say that we have a collection of DNA strings, all having the same length n. Their profile matrix is a 4×n matrix P in which P1,j represents the number of times that 'A' occurs in the jth position of one of the strings, P2,j represents the number of times that C occurs in the jth position, and so on (see below).
# A consensus string c is a string of length n formed from our collection by taking the most common symbol at each position; the jth symbol of c therefore corresponds to the symbol having the maximum value in the j-th column of the profile matrix. Of course, there may be more than one most common symbol, leading to multiple possible consensus strings.
# Given: A collection of at most 10 DNA strings of equal length (at most 1 kbp) in FASTA format.
# Return: A consensus string and profile matrix for the collection. (If several possible consensus strings exist, then you may return any one of them.)
# Sample Dataset
# >Rosalind_1
# ATCCAGCT
# >Rosalind_2
# GGGCAACT
# >Rosalind_3
# ATGGATCT
# >Rosalind_4
# AAGCAACC
# >Rosalind_5
# TTGGAACT
# >Rosalind_6
# ATGCCATT
# >Rosalind_7
# ATGGCACT
# Sample Output
# ATGCAACT
# A: 5 1 0 0 5 5 0 0
# C: 0 0 1 4 2 0 6 1
# G: 1 1 6 3 0 1 0 0
# T: 1 5 0 0 0 1 1 6
# 这道题的目标是找到DNA序列集合中，每个位置出现次数最多的字符，将这些字符组合成一个新的字符串并称之为共识串。同时需要输出一个矩阵，矩阵的第i行第j列表示在i位置上的A,C,G,T出现的次数。
# 代码：
def consensus_and_profile(dna_strings):
# 计算每个位置上的字符出现次数
profile = {'A': [0] *len(dna_strings[0]),
'C': [0] *len(dna_strings[0]),
'G': [0] *len(dna_strings[0]),
'T': [0] *len(dna_strings[0])}
for dnain dna_strings:
for iin range(len(dna)):
profile[dna[i]][i] +=1
# 生成共识串
consensus =''
for iin range(len(dna_strings[0])):
max_count =0
max_char =''
for charin ['A', 'C', 'G', 'T']:
if profile[char][i] > max_count:
max_count = profile[char][i]
max_char = char
consensus += max_char
return consensus, profile
# 读入数据集
data_file =open("input.txt", "r")
dna_strings = []
current_dna =''
for linein data_file:
if line[0] =='>':# 新的DNA序列开始
if current_dna !='':
dna_strings.append(current_dna)
current_dna =''
else:
current_dna += line.strip()
dna_strings.append(current_dna)# 最后一个DNA序列
data_file.close()
# 计算共识串和计数矩阵
consensus, profile = consensus_and_profile(dna_strings)
# 输出结果
print(consensus)
for charin ['A', 'C', 'G', 'T']:
print(char +':', ' '.join(str(x)for xin profile[char]))
