Creating a Character Table from Genetic Strings

https://rosalind.info/problems/cstr/

ROSALIND | Creating a Character Table from Genetic Strings

 

Problem

A collection of strings is characterizable if there are at most two possible choices for the symbol at each position of the strings.

Given: A collection of at most 100 characterizable DNA strings, each of length at most 300 bp.

Return: A character table for which each nontrivial character encodes the symbol choice at a single position of the strings. (Note: the choice of assigning '1' and '0' to the two states of each SNP in the strings is arbitrary.)

Sample Dataset

ATGCTACC
CGTTTACC
ATTCGACC
AGTCTCCC
CGTCTATC

Sample Output

10110
10100

 

 이 문제는 SNP를 기준으로 캐릭터라이징을 하는 문제이다. 단순하게 첫번째 문자열을 기준으로 문자가 같으면 1 아니면 0인 식으로 하면 된다.

def make_ch_table(seqs):
    ch_table=set()

    for idx,nuc in enumerate(seqs[0]):
        ch_array = [int(nuc==seq[idx]) for seq in seqs]
        if 1<sum(ch_array)<len(ch_array)-1:
            ch_table.add(''.join(map(str,ch_array)))
    
    return ch_table

if __name__ == '__main__':
    with open(r"파일경로",'r') as f:
        seqs=[]
        for i in f.readlines():
            seqs.append(i.rstrip())

ch_table = make_ch_table(seqs)

with open(r"파일경로",'w') as wf:
    wf.write('\n'.join(ch_table))