【Rosalind】Consensus and Profile

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该博客介绍了如何处理一组等长DNA序列，通过统计每个位置上不同碱基（A、C、G、T）出现的频率，生成一个共识字符串和对应的碱基频率矩阵。给出的参考代码使用Python的Bio库解析FASTA格式的DNA序列，并输出最常见的碱基及其在每个位置的计数。

问题描述

Problem

A matrix is a rectangular table of values divided into rows and columns. An $\times n$ matrix has $m$ rows and $n$ columns. Given a matrix $A$ , we write $A_{i, j}$ 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 $\times n$ matrix $P$ in which $P_{1,j}$ represents the number of times that ‘A’ occurs in the $j$ th position of one of the strings, $P_{2,j}$ represents the number of times that C occurs in the $j$ th 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 $j$ th 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.

DNA Strings
A T C C A G C T
G G G C A A C T
A T G G A T C T
A A G C A A C C
T T G G A A C T
A T G C C A T T
A T G G C A C T
Profile
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
Consensus
A T G C A A C T

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

题目大意

给多串等长DNA序列，统计各位置不同碱基出现的次数，第一行输出各位置上最常见的碱基（如有多个，输出任意一个），接下来4行输出各位置各碱基出现的次数

题解

生成一个链表，每一项为一个字典，统计各位置各碱基出现的次数，最后输出即可
注意输入数据满足fasta格式，可能存在一个序列碱基有多行的情况，注意处理

参考代码

from Bio import SeqIO

l = 0
ans = []

for seq_record in SeqIO.parse("rosalind_cons.txt", "fasta"):
	if (l == 0):
		l = len(seq_record.seq)
		for i in range(l):
			ans.append({'A': 0, 'G': 0, 'C': 0, 'T':0})
	for i in range(l):
		ans[i][seq_record.seq[i]] += 1

with open("out.txt", "w") as fo:
	for i in range(l):
		fo.write(max(ans[i], key = ans[i].get))
	fo.write('\n')
	for j in ['A', 'C', 'G', 'T']:
		fo.write("%s: " % j)
		for i in range(l):
			fo.write("%d " % ans[i][j])
		fo.write("\n")
	fo.close()