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generator.py
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generator.py
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#!/usr/bin/python3
import string
import random
import math
from random import randint
def generate(fragmentsDir, genomeDir, id, genomeSize = 1000, fragmentMinSize = 35, fragmentMaxSize = 50, coverage = 2):
random.seed(1234 * id)
# Calcula o numero de fragmentos dada a cobertura
numFragments = math.ceil(genomeSize / ((fragmentMinSize + fragmentMaxSize)/2) * coverage)
def id_generator(size=6, chars=string.ascii_uppercase + string.digits):
return ''.join(random.choice(chars) for _ in range(size))
# Gera sequência
genome = id_generator(genomeSize, "ACTG")
# Escreve sequência
file = open(genomeDir + str(id) + ".txt", "w+")
file.write(genome)
file.close()
file = open(fragmentsDir + str(id) + ".txt", "w+")
print("Tamanho Sequência Original:", len(genome))
added = []
for i in range (0, numFragments):
index = randint(0, genomeSize - fragmentMaxSize)
fragment = genome[index:index+randint(fragmentMinSize, fragmentMaxSize)]
if (fragment not in added):
file.write(fragment + "\n")
added.append(fragment)
file.close()