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encode.py
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encode.py
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"""
Copyright (C) 2016 Yaniv Erlich
License: GPLv3-or-later. See COPYING file for details.
"""
from distutils.core import setup
from Cython.Build import cythonize
from fountain import DNAFountain
from utils import screen_repeat, restricted_float, prepare
import argparse
import logging
import Colorer
import os
import sys
#from sets import Set
from lfsr import lfsr
import json
from tqdm import tqdm
from preprocessing import read_file, read_file_np
import timeit
logging.basicConfig(level=logging.DEBUG)
def read_args():
parser = argparse.ArgumentParser()
parser.add_argument("-f", "--file_in", help="file to encode", required = True)
parser.add_argument("-l", "--size", help="number of information bytes per message", default = 128, type = int)
parser.add_argument("-m", "--max_homopolymer", help="the largest number of nt in a homopolymer", default = 4, type = int)
parser.add_argument("--gc", help="the fraction of gc content above/below 0.5 (example:0.1 means 0.4-0.6)", default = 0.2, type = restricted_float)
parser.add_argument("--rs", help="Number of bytes for rs codes", default = 0, type = int)
parser.add_argument("--delta", help="Degree distribution tuning parameter", default = 0.05, type = float)
parser.add_argument("--c_dist", help = "Degree distribution tuning parameter", default = 0.1, type = float)
parser.add_argument("--out", help = "File with DNA oligos", required = True)
parser.add_argument("--stop", help = "Maximal number of oligos", default = None, type = int)
parser.add_argument("--alpha", help = "How many more fragments to generate on top of first k (example: 0.1 will generate 10 percent more fragments)", default = 0.07, type = float)
parser.add_argument("--no_fasta", help = "Print oligo without a fasta header", default = False, action='store_true')
parser.add_argument("--rand_numpy", help = "Uses numpy random generator. Faster but not compatible with older versions", default = False, action = 'store_true')
args = parser.parse_args()
args.orf= None
return(args)
def main():
args = read_args()
logging.info("Reading the file. This may take a few mintues")
f_in, file_size = read_file(args.file_in, args.size)
f = DNAFountain(file_in = f_in,
file_size = file_size,
chunk_size = args.size ,
rs = args.rs,
max_homopolymer = args.max_homopolymer,
gc = args.gc,
delta = args.delta,
c_dist = args.c_dist,
np = args.rand_numpy,
alpha = args.alpha,
stop = args.stop)
logging.info("Upper bounds on packets for decoding is %d (x%f) with %f probability\n", int(json.loads(f.PRNG.debug())['K_prime']),
json.loads(f.PRNG.debug())['Z'],
json.loads(f.PRNG.debug())['delta'])
if (args.out == '-'):
out = sys.stdout
else:
out = open (args.out, 'w')
pbar = tqdm(total= f.final, desc = "Valid oligos")
prepare(args.max_homopolymer)
used_bc = dict()
while f.good < f.final:
print('f.good',f.good,'f.final',f.final)
d = f.droplet()
#print('droplet is',d)
print('f.screen(d) is', f.screen(d))
if f.screen(d):
print('in f.screen, d is',d)
if not args.no_fasta:
out.write(">packet {}_{}\n".format(f.good, d.degree))
out.write("{}\n".format(d.to_human_readable_DNA()))
if d.seed in used_bc:
logging.error("Seed %d has been seen before\nDone", d.seed)
sys.exit(1)
used_bc[d.seed] = 1
if (args.out != '-'):
pbar.update()
if (args.out != '-'):
pbar.close()
logging.info("Finished. Generated %d packets out of %d tries (%.3f)", f.good, f.tries, (f.good+0.0)/f.tries)
out.close()
main()