共识字符串和配置文件矩阵

Question

我已经编写了以下 python 代码来解决 Rosalind 的一个问题 (http://rosalind.info/problems/cons/)，出于某种原因，Rosalind 说答案是错误的，但我做了一些抽查并且它似乎正确。

问题如下：

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.)

样本数据集是：

>Rosalind_1
ATCCAGCT
>Rosalind_2
GGGCAACT
>Rosalind_3
ATGGATCT
>Rosalind_4
AAGCAACC
>Rosalind_5
TTGGAACT
>Rosalind_6
ATGCCATT
>Rosalind_7
ATGGCACT

示例解决方案是：

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

我尝试解决这个问题：

from Bio import SeqIO

A,C,G,T = [],[],[],[]
consensus=""

for i in range(0,len(record.seq)):
    countA,countC,countG,countT=0,0,0,0
    for record in SeqIO.parse("fasta.txt", "fasta"):
        if record.seq[i]=="A":
            countA=countA+1
        if record.seq[i]=="C":
            countC=countC+1
        if record.seq[i]=="G":
            countG=countG+1
        if record.seq[i]=="T":
            countT=countT+1

    A.append(countA)
    C.append(countC)
    G.append(countG)
    T.append(countT)

    if countA >= max(countC,countG,countT):
        consensus=consensus+"A"
    elif countC >= max(countA,countG,countT):
        consensus=consensus+"C"
    elif countG >= max(countA,countC,countT):
        consensus=consensus+"G"
    elif countT >= max(countA,countC,countG):
        consensus=consensus+"T"

print("A: "+" ".join([str(i) for i in A]))
print("C: "+" ".join([str(i) for i in C]))
print("G: "+" ".join([str(i) for i in G]))
print("T: "+" ".join([str(i) for i in T]))

print(consensus)

如果有人可以看一下并提出我做错了什么，那就太好了？非常感谢！

Answer 1

对于您的共识字符串，您的代码未处理您有平局的情况，即给定位置的两个核苷酸出现频率相同。您现在编写代码的方式，这种情况将导致在共识字符串

中的那个位置不打印任何内容

Answer 2

这部分

 if countA >= max(countC,countG,countT):
            consensus=consensus+"A"
        elif countC >= max(countA,countG,countT):
            consensus=consensus+"C"
        elif countG >= max(countA,countC,countT):
            consensus=consensus+"G"
        elif countT >= max(countA,countC,countG):
            consensus=consensus+"T"

改用它，您将正确获得共识序列

if countA[i] >= max(countC[i],countG[i],countT[i]):
      consensus+="A"
  if countC[i] >= max(countA[i],countG[i],countT[i]):
      consensus+="C"     
  if countG[i] >= max(countA[i],countC[i],countT[i]):
      consensus+="G"
  if countT[i] >= max(countA[i],countC[i],countG[i]):
      consensus+="T"

共识字符串和配置文件矩阵

Consensus string & profile matrix

python

rosalind