[Rosalind] RNA Splicing (Python)

Problem

 

Given: fasta 형식으로 이루어진 대략 1000 길이의 DNA 서열과, 서열의 intron 서열

Return: S의 exon부분이 전사 된 단백질 서열

Sample Dataset

>Rosalind_10
ATGGTCTACATAGCTGACAAACAGCACGTAGCAATCGGTCGAATCTCGAGAGGCATATGGTCACATGATCGGTCGAGCGTGTTTCAAAGTTTGCGCCTAG
>Rosalind_12
ATCGGTCGAA
>Rosalind_15
ATCGGTCGAGCGTGT

Sample Output

MVYIADKQHVASREAYGHMFKVCA

예제 데이터 풀이

1. RNA서열에서 Intron 서열을 제외한다.

2. 남은 Exon서열을 protein으로 번역한다.

 

풀이

## 1. 파일 읽기 
import re, sys, os

# 2. Import sequence
with open('./rosalind_splc.txt', 'r') as f :
    lines = f.readlines()

# 3. seq to dictionary
id_pattern = re.compile('>(\S+)')

Seq_d = {}
for line in lines:
        outh = id_pattern.search(line)
        if outh:
                Seq_id=outh.group(1)
        else:
                outl=line
                if(Seq_id in Seq_d.keys()):
                        Seq_d[Seq_id] += line.replace('\n', '')
                else:
                        Seq_d[Seq_id]  =line.replace('\n', '')


# 4. codon to amino
amino = {'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M', 
         'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T', 
         'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K', 
         'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
         'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', 
         'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', 
         'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q', 
         'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R', 
         'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', 
         'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A', 
         'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E', 
         'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
         'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', 
         'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
         'TAC':'Y', 'TAT':'Y', 'TAA':'', 'TAG':'', 
         'TGC':'C', 'TGT':'C', 'TGA':'', 'TGG':'W' }

5. RNA splicing
def RNA_splicing(Seq_d):
    i= 0
    for seq in Seq_d.values() : 
        if i == 0 : 
            i = i+1
            RNA = seq
        else : 
            RNA = RNA.replace(seq, '')

    return RNA
    
# 6. Exon rna to protein
def protein_print(RNA, amino):
    for i in range(0, len(RNA), 3):
        codon = RNA[i:(i + 3)]
        am = amino.get(codon, '')
        if am:
            print(am, end="")
        else:
            print("Stop")
            break

# 7. Run
RNA = RNA_splicing(Seq_d)
protein_print(RNA, amino)

 

 

다른 솔루션  by Laperche Sylvain

#!/usr/bin/env python3

from re import sub
from RNA import rna_transcription
from PROT import translate

def splicing(dna, introns):
    pattern = '|'.join([ '(' + intron + ')' for intron in introns ])
    return translate(rna_transcription(sub(pattern, '', dna)))

if __name__ == '__main__':
    with open('SPLC.dataset', encoding='utf-8') as dataset:
        dna = dataset.readline().rstrip()
        introns = [ intron.rstrip() for intron in dataset.readlines() ]
    print(splicing(dna, introns))