I have written the following python code to solve one of the Rosalind problems (http://rosalind.info/problems/cons/) and for some reason, Rosalind says the answer is wrong but I did some spot-checking and it appears right.
The problem is as follows:
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.)
A sample dataset is:
>Rosalind_1
ATCCAGCT
>Rosalind_2
GGGCAACT
>Rosalind_3
ATGGATCT
>Rosalind_4
AAGCAACC
>Rosalind_5
TTGGAACT
>Rosalind_6
ATGCCATT
>Rosalind_7
ATGGCACT
A sample solution is:
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
My attempt to solve this:
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)
Would be great if someone can take a look and suggest what I am doing wrong? Many thanks!
For your consensus string, your code is not handling the case in which you have a tie, i.e., two nucleotides in a given position are equally frequent. The way your code is written now, this case will result in nothing being printed at that position in the consensus string