# replace+genomes.py
# -----------------------------------------------------------------------------
# DanB 4/7/2021
# -----------------------------------------------------------------------------
import time
import os
import argparse
import numpy
import emod_api.serialization.SerializedPopulation as SerPop
from pathlib import Path
import importlib
[docs]class Genome:
"""
Represent a single genome
"""
[docs] def convert_char_to_int(ch):
if ch == 'A':
return 0
elif ch == 'C':
return 1
elif ch == 'G':
return 2
elif ch == 'T':
return 3
else:
raise Exception("Unknown character ch=" + ch)
[docs] def create_genome(barcode_str, allele_root_id):
g = Genome()
g.barcode_str = barcode_str
g.hash_code = 17 # must match value in C++ code, see file ParasiteGnome.cpp
g.barcode_hash_code = 17 # must match value in C++ code, see file ParasiteGnome.cpp
for ch in barcode_str:
val = Genome.convert_char_to_int(ch)
g.nucleotides.append(val)
g.allele_roots.append(allele_root_id)
g.barcode_hash_code = numpy.int32(31 * g.barcode_hash_code + val)
g.hash_code = numpy.int32(31 * g.hash_code + val)
g.hash_code = numpy.int32(31 * g.hash_code + allele_root_id)
return g
def __init__(self):
self.hash_code = numpy.int32(0)
self.barcode_hash_code = numpy.int32(0)
self.allele_roots = []
self.nucleotides = []
self.barcode_str = ""
@property
def barcode(self):
return self.barcode_str
@property
def hashcode(self):
return self.hash_code
[docs] def set_allele_roots(self, root):
if len(self.allele_roots) > 0:
raise Exception("Allele Roots already set")
for val in self.nucleotides:
self.allele_roots.append(root)
[docs] def to_dtk_dict(self):
dtk_dict = {}
dtk_dict["m_pInner"] = {}
dtk_dict["m_pInner"]["__class__"] = "ParasiteGenomeInner"
dtk_dict["m_pInner"]["m_HashCode"] = int(self.hash_code)
dtk_dict["m_pInner"]["m_BarcodeHashcode"] = int(self.barcode_hash_code)
dtk_dict["m_pInner"]["m_NucleotideSequence"] = self.nucleotides
dtk_dict["m_pInner"]["m_AlleleRoots"] = self.allele_roots
return dtk_dict
[docs] def to_dtk_map_entry(self):
dtk_map_entry = {}
dtk_map_entry["key"] = int(self.hash_code)
dtk_map_entry["value"] = {}
dtk_map_entry["value"] = self.to_dtk_dict()["m_pInner"]
return dtk_map_entry
[docs]def print_hashcodes(ser_pop):
for genome in ser_pop.dtk.simulation["ParasiteGenetics"]["m_ParasiteGenomeMap"]:
print(genome.key)
for node in ser_pop.nodes:
for person in node["individualHumans"]:
print("------------ " + str(person["suid"]["id"]) + " -----------------")
for infection in person["infections"]:
print(infection["infection_strain"]["m_Genome"]["m_pInner"]["m_HashCode"])
for vector_pop in node["m_vectorpopulations"]:
for vector in vector_pop["AdultQueues"]:
print("------------ VECTOR " + str(vector["m_ID"]) + " -----------------")
for oocyst in vector["m_OocystCohorts"]:
print("oocyst-male=" + str(oocyst["m_MaleGametocyteGenome"]["m_pInner"]["m_HashCode"])
+ "--- "
+ "oocyst-female=" + str(oocyst["m_pStrainIdentity"]["m_Genome"]["m_pInner"]["m_HashCode"]))
for sporo in vector["m_SporozoiteCohorts"]:
print("sporo-male=" + str(sporo["m_MaleGametocyteGenome"]["m_pInner"]["m_HashCode"])
+ "--- "
+ "sporo-female=" + str(sporo["m_pStrainIdentity"]["m_Genome"]["m_pInner"]["m_HashCode"]))
[docs]def get_next_genome(next_barcode_fn, allele_root_id, ser_pop_genome_map, cache_genome_map):
barcode_str = next_barcode_fn()
key = barcode_str + "-" + str(allele_root_id)
if key in cache_genome_map:
genome = cache_genome_map[key]
else:
genome = Genome.create_genome(barcode_str, allele_root_id)
cache_genome_map[key] = genome
ser_pop_genome_map.append(genome.to_dtk_map_entry())
dtk_genome_obj = genome.to_dtk_dict()
# print(genome.barcode + "=" + str(genome.hashcode))
return dtk_genome_obj
[docs]def replace_genomes(input_file, next_barcode_fn, output_file):
"""
Replaces genomes in infected individuals and vectors.
Args:
input_file: Input serialized population file
next_barcode_fn: Function that return the next barcode. The function is called once for every infection of an
individual and once for every vector in the vector population.
output_file: Output file with replaced genomes.
Returns:
Nothing
"""
if not os.path.exists(input_file):
raise Exception(f"Couldn't find specified input file: {input_file}.")
if next_barcode_fn is None:
raise Exception("You must provide a function that returns the next barcode string")
pop = SerPop.SerializedPopulation(input_file)
ser_pop_genome_map = pop.dtk.simulation["ParasiteGenetics"]["m_ParasiteGenomeMap"]
ser_pop_genome_map.clear()
cache_genome_map = {}
for node in pop.nodes:
# tic1 = time.perf_counter()
for person in node["individualHumans"]:
# print("------------ " + str(person["suid"]["id"]) + " -----------------")
for infection in person["infections"]:
next_genome = get_next_genome(next_barcode_fn, person["suid"]["id"], ser_pop_genome_map,
cache_genome_map)
length_barcode = len(infection["infection_strain"]["m_Genome"]["m_pInner"]["m_NucleotideSequence"])
assert length_barcode == len(
next_genome["m_pInner"]["m_NucleotideSequence"]), f"New barcode has wrong length."
infection["infection_strain"]["m_Genome"] = next_genome
# tic2 = time.perf_counter()
# print(f"{tic2 - tic1:0.4f}")
for vector_pop in node["m_vectorpopulations"]:
# print(len(vector_pop["AdultQueues"]))
# tic1 = time.perf_counter()
for vector in vector_pop["AdultQueues"]["collection"]:
# print("------------ VECTOR " + str(vector["m_ID"]) + " -----------------")
for oocyst in vector["m_OocystCohorts"]:
genome_oocyst = get_next_genome(next_barcode_fn, -999, ser_pop_genome_map, cache_genome_map)
length_oocyst_barcode = len(oocyst["m_MaleGametocyteGenome"]["m_pInner"]["m_NucleotideSequence"])
assert len(genome_oocyst["m_pInner"][
"m_NucleotideSequence"]) == length_oocyst_barcode, f"New barcode has wrong length."
oocyst["m_MaleGametocyteGenome"] = genome_oocyst
genome_oocyst = get_next_genome(next_barcode_fn, -999, ser_pop_genome_map, cache_genome_map)
length_oocyst_barcode = len(
oocyst["m_pStrainIdentity"]["m_Genome"]["m_pInner"]["m_NucleotideSequence"])
assert len(genome_oocyst["m_pInner"][
"m_NucleotideSequence"]) == length_oocyst_barcode, f"New barcode has wrong length."
oocyst["m_pStrainIdentity"]["m_Genome"] = genome_oocyst
for sporo in vector["m_SporozoiteCohorts"]:
genome_sporo = get_next_genome(next_barcode_fn, -999, ser_pop_genome_map, cache_genome_map)
length_sporo_barcode = len(sporo["m_MaleGametocyteGenome"]["m_pInner"]["m_NucleotideSequence"])
assert len(genome_sporo["m_pInner"][
"m_NucleotideSequence"]) == length_sporo_barcode, f"New barcode has wrong length."
sporo["m_MaleGametocyteGenome"] = genome_sporo
genome_sporo = get_next_genome(next_barcode_fn, -999, ser_pop_genome_map, cache_genome_map)
length_sporo_barcode = len(
sporo["m_pStrainIdentity"]["m_Genome"]["m_pInner"]["m_NucleotideSequence"])
assert len(genome_sporo["m_pInner"][
"m_NucleotideSequence"]) == length_sporo_barcode, f"New barcode has wrong length."
sporo["m_pStrainIdentity"]["m_Genome"] = genome_sporo
# tic2 = time.perf_counter()
# print(f"{tic2 - tic1:0.4f}")
pop.write(output_file)
[docs]def test_replace_genomes(input_fn, get_next_barcode):
if not os.path.exists(input_fn):
raise Exception(f"Couldn't find specified input file: {input_fn}.")
pop = SerPop.SerializedPopulation(input_fn)
for node in pop.nodes:
for person in node["individualHumans"]:
for infection in person["infections"]:
genome_as_int = list(map(Genome.convert_char_to_int, get_next_barcode()))
assert infection["infection_strain"]["m_Genome"]["m_pInner"]["m_NucleotideSequence"] == genome_as_int
for vector_pop in node["m_vectorpopulations"]:
for vector in vector_pop["AdultQueues"]["collection"]:
for oocyst in vector["m_OocystCohorts"]:
genome_as_int = list(map(Genome.convert_char_to_int, get_next_barcode()))
assert oocyst["m_MaleGametocyteGenome"]["m_pInner"]["m_NucleotideSequence"] == genome_as_int
genome_as_int = list(map(Genome.convert_char_to_int, get_next_barcode()))
assert oocyst["m_pStrainIdentity"]["m_Genome"]["m_pInner"]["m_NucleotideSequence"] == genome_as_int
for sporo in vector["m_SporozoiteCohorts"]:
genome_as_int = list(map(Genome.convert_char_to_int, get_next_barcode()))
assert sporo["m_MaleGametocyteGenome"]["m_pInner"]["m_NucleotideSequence"] == genome_as_int
genome_as_int = list(map(Genome.convert_char_to_int, get_next_barcode()))
assert sporo["m_pStrainIdentity"]["m_Genome"]["m_pInner"]["m_NucleotideSequence"] == genome_as_int
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Replace genomes.",
epilog="E.g. python replace_genomes.py -i state-00050.dtk -o low_eir_no_DR.dtk -m replace_genomes_get_next_barcode -f get_next_barcode")
parser.add_argument("-i", "--input_file", type=Path, required=True, help="Serialized population file.")
parser.add_argument("-o", "--output_file", type=Path, required=True, help="Serialized population output file.")
parser.add_argument("-m", "--module", type=str, default="replace_genomes_get_next_barcode",
help="Module that contains the function to generate the barcodes.")
parser.add_argument("-f", "--get_next_barcode_func", type=str, default="get_next_barcode",
help="Name of the function that returns the barcodes")
args = parser.parse_args()
try:
user_defined_mod = importlib.import_module(args.module)
except ModuleNotFoundError as err:
print(err)
print("Current working directory:", os.getcwd())
exit(-1)
replace_genomes(args.input_file, eval("user_defined_mod." + args.get_next_barcode_func), args.output_file)
# importlib.reload(user_defined_mod) # reimport module to reinitialize variables in module containing function to get next barcode
# test_replace_genomes(args.output_file, eval("user_defined_mod." + args.get_next_barcode_func))
