#!/usr/bin/env python3
import sys
import os
import shutil
import random
import argparse
import traceback
from collections import OrderedDict
import vcf
from Bio import SeqIO
import tempfile
from pysam import tabix_compress, tabix_index, VariantFile
from variants_simulator import VariantsSimulator
from exceptions import InputException, ExecException
import multiprocessing
import subprocess
class Print:
def __init__(self, stdout=None, stderr=None):
self.stdout = stdout
self.stderr = stderr
if self.stdout is not None and os.path.isfile(self.stdout):
os.remove(self.stdout)
if self.stderr is not None and os.path.isfile(self.stderr):
os.remove(self.stderr)
def out(self, message):
if self.stdout is not None:
with open(self.stdout, "a") as stdout_f:
print(message, file=stdout_f)
else:
print(message, file=sys.stdout)
def err(self, message):
if self.stderr is not None:
with open(self.stderr, "a") as stderr_f:
print(message, file=stderr_f)
else:
print(message, file=sys.stderr)
def check_min_size(value):
ivalue = int(value)
if ivalue <= 1:
raise argparse.ArgumentTypeError("%s is an invalid size value (>= 1)" % value)
return ivalue
def parse_args():
"""
Parse script arguments
:return: argparse arguments object
"""
parser = argparse.ArgumentParser(description='Generate simulated populations with SV',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("-n", "--nb-inds", help="Number of individuals to generate", type=int)
parser.add_argument("-r", "--reference", help="Reference genome", required=True)
parser.add_argument("-ns", "--nstretches", help="N-stretches positions bed file")
parser.add_argument("-s", "--sv-list", help="File containing the SVs", required=False)
parser.add_argument("-c", "--coverage", help="Coverage of reads", default=15, type=int)
parser.add_argument("-o", "--output-directory", help="Output directory", default="res")
parser.add_argument("-e", "--force-outputdir", help="Delete output directory before start, if already exists",
action='store_const', const=True, default=False)
parser.add_argument("-f", "--force-polymorphism", help="Force polymorphism for each SV", action='store_const',
const=True, default=False)
parser.add_argument("-a", "--haploid", help="Make a haploid genome, instead of diploid one", action="store_const",
const=True, default=False)
parser.add_argument("-p", "--proba-del", help="Probabilty to have a deletion", type=float, default=0.000001)
parser.add_argument("-l", "--read-len", help="Generate reads having a length of LEN", type=int, default=100)
parser.add_argument("-m", "--insert-len-mean", help="Generate inserts (fragments) having an average length of LEN",
type=int, default=300)
parser.add_argument("-v", "--insert-len-sd", help="Set the standard deviation of the insert (fragment) length (%%)",
type=int, default=30)
parser.add_argument("-q", "--quiet", help="Don't ask anything, choose default answer instead", action="store_const",
const=True, default=False)
parser.add_argument("-md", "--min-deletions", help="Minimum of deletions to generate (>=1)", default=1,
type=check_min_size)
parser.add_argument("-t", "--threads", help="Number of threads", default=multiprocessing.cpu_count(), type=int)
parser.add_argument("-g", "--genotypes", help="Position of SV with genotypes of individuals")
args = parser.parse_args()
if args.nb_inds is None and args.genotypes is None:
parser.error("--nb-inds parameter is required (except if --genotypes parameter is given)")
return args
def _allele(frequency):
"""
Get randomly an allele, given a frequency
:param frequency: frequency of the allele {float}
:return: allele randomly choosen {0 or 1}
"""
return 1 if random.uniform(0, 1) < frequency else 0
def _get_genotypes_for_inds(nb_inds, haploid, freq):
"""
Get genotypes for each individual
:param nb_inds: number of individuals {int}
:param haploid: is the genome hamploid {bool}
:param freq: frequency of the allele {float}
:return: list of genotypes, vcf data {list}
"""
all_genotypes = []
genotypes_row = []
for i in range(1, nb_inds + 1):
if not haploid:
genotype = str(_allele(freq)) + "/" + str(_allele(freq))
else:
genotype = str(_allele(freq))
genotype_data = vcf.model._Call(None, "indiv" + str(i), vcf.model.make_calldata_tuple("GT")(GT=genotype))
genotypes_row.append(genotype_data)
all_genotypes.append(genotype)
return all_genotypes, genotypes_row
def _svsort(sv, chrm, genotypes_for_inds):
"""
Function to sort regions
:param sv: the variant
:param chrm: chromosome {str}
:param genotypes_for_inds: dictionary of genotypes for each individual
"""
return int(genotypes_for_inds[chrm][sv]["start"])
def _build_vcf_header(vcf_file, prg_path, tmp_dir, nb_inds):
"""
Build header of the VCF file
:param vcf_file: vcf file full path name {str}
:param prg_path: program path {str}
:param tmp_dir: temporary directory {str}
:param nb_inds: number of individuals {int}
"""
try:
with open(os.path.join(prg_path, "template.vcf"), "r") as template:
try:
with open(vcf_file, "w") as my_template:
for line in template:
if line[:6] == "#CHROM":
line = line.replace("\n", "")
for i in range(0, nb_inds):
line += "\tindiv" + str(i+1)
line += "\n"
my_template.write(line)
except IOError:
raise ExecException("ERROR: unable to create template file \"{0}\" in temp dir.".
format(os.path.join(tmp_dir, "template.vcf")))
except IOError:
raise ExecException("ERROR: template file not found in program directory.")
def build_genotypes_vcf_list(deletions: dict, output_vcf, haploid, force_polymorphism, nb_inds, tmp_dir, prg_path):
"""
Build VCF file describing genotypes for each individual (and the associated python dictionary)
:param deletions: deletions description {dict}
:param output_vcf: output VCF file full path name {str}
:param haploid: is haploid {bool}
:param force_polymorphism: force polymorphism {bool}
:param nb_inds: number of individuals {int}
:param tmp_dir: temporary directory {str}
:param prg_path: program path {str}
:return: dictionary of genotypes for each variant for each dictionary {OrderedDict}
"""
genotypes_for_inds = OrderedDict()
# { chr: { id_indiv: {start: #start, end: #end, genotypes: [[0,1],[1,1],...], ...}, # ...}
vcf_file = os.path.join(tmp_dir, "template.vcf")
# Build VCF header:
_build_vcf_header(vcf_file, prg_path, tmp_dir, nb_inds)
vcf_reader = vcf.Reader(filename=vcf_file)
vcf_writer = vcf.Writer(open(output_vcf, "w"), vcf_reader)
for chrm, deletes in deletions.items():
for delete in deletes:
if chrm not in genotypes_for_inds:
genotypes_for_inds[chrm] = {}
genotypes_for_inds[chrm][delete["name"]] = {"start": delete["start"], "end": delete["end"], "genotypes": []}
# Get genotypes:
all_genotypes, genotypes = [], []
if force_polymorphism:
polymorph = False
while not polymorph:
all_genotypes, genotypes = _get_genotypes_for_inds(nb_inds, haploid, delete["freq"])
polymorph = len(set(all_genotypes)) > 1
else:
all_genotypes, genotypes = _get_genotypes_for_inds(nb_inds, haploid, delete["freq"])
genotypes_for_inds[chrm][delete["name"]]["genotypes"] = [x.split("/") for x in all_genotypes]
info = {"END": delete["end"], "AF": delete["freq"]}
vcf_record = vcf.model._Record(chrm, delete["start"], delete["name"], "N", [vcf.model._SV("DEL")], ".",
".", info, "GT", [0], genotypes)
vcf_writer.write_record(vcf_record)
vcf_writer.close()
tabix_compress(output_vcf, output_vcf + ".gz", True)
tabix_index(output_vcf + ".gz", force=True, preset="vcf")
os.remove(output_vcf)
return genotypes_for_inds
def load_genotypes_from_file(genotypes_file):
variants = VariantFile(genotypes_file)
genotypes_for_inds = {}
nb_inds = 0
for variant in variants:
chrm = variant.chrom
id_v = variant.id
start = variant.start
end = variant.stop
samples = variant.samples
gt = [list(map(str, samples[x]["GT"])) for x in samples]
if chrm not in genotypes_for_inds:
genotypes_for_inds[chrm] = {}
genotypes_for_inds[chrm][id_v] = {
"start": start,
"end": end,
"genotypes": gt
}
nb_inds = len(gt)
return nb_inds, genotypes_for_inds
def _compute_keeped_genomic_regions(svs, svs_infos, haploid):
"""
Get list of all regions keeped (not deleted)
:param svs: list of variants (deletions) {list}
:param svs_infos: infos of variants {dict}
:param haploid: is haploid {bool}
:return: regions for each individuals {OrderedDict}, the last position for each region {OrderedDict}
"""
regions = OrderedDict()
current_region_pointer = OrderedDict()
for svs_i in svs:
i = 0
for genotypes in svs_infos[svs_i]["genotypes"]:
if i not in regions:
regions[i] = {}
current_region_pointer[i] = {}
for j in range(0, 2 if not haploid else 1): # For each chromosome of the diploid genome, or the chromosome
# of the haploid genome
if j not in regions[i]:
regions[i][j] = []
current_region_pointer[i][j] = "0"
if svs_infos[svs_i]["genotypes"][i][j] == "1":
regions[i][j].append([current_region_pointer[i][j], svs_infos[svs_i]["start"]])
current_region_pointer[i][j] = svs_infos[svs_i]["end"]
i += 1
return regions, current_region_pointer
def _build_fastas(chrm, regions, current_region_pointer, output_dir, fasta_orig_chr, last_nt):
"""
Build fasta files
:param chrm:
:param regions:
:param current_region_pointer:
:param output_dir:
:param fasta_orig_chr:
:param last_nt:
:return:
"""
for indiv, chrs_dips in regions.items():
id_chrs = list(chrs_dips.keys())
id_chrs = sorted(id_chrs)
for id_chr in id_chrs:
chr_dip = chrs_dips[id_chr] # SVs for each diploid chromosome
logs_regions = [] # Store logs
# Build FASTA and store logs:
try:
with open(os.path.join(output_dir, "indiv" + str(indiv + 1) + "_chr_" + str(id_chr) + ".fasta"),
"a") as output_handle:
fasta = ""
last_one = 0
for chr_region in chr_dip:
fasta += fasta_orig_chr[int(chr_region[0]):int(chr_region[1])]
logs_regions.append("\t".join(str(x) for x in chr_region))
last_one = int(chr_region[1])
if last_one < last_nt:
logs_regions.append("\t".join([str(current_region_pointer[indiv][id_chr]), str(last_nt)]))
fasta += fasta_orig_chr[int(current_region_pointer[indiv][id_chr]):last_nt]
SeqIO.write(fasta, output_handle, "fasta")
except IOError:
raise ExecException("ERROR: unable to write \"{0}\" file.".
format(os.path.join(output_dir, "indiv" + str(indiv + 1) + "_chr_" + str(id_chr) +
".fasta")))
# Write logs
try:
with open(os.path.join(output_dir, "indiv" + str(indiv + 1) + ".regions.log"), "a") as log_handle:
log_handle.write(chrm + "_" + str(id_chr) + "\t")
log_handle.write("\n\t".join(logs_regions))
log_handle.write("\n")
except IOError:
raise ExecException("ERROR: unable to write log file: \"{0}\"".
format(os.path.join(output_dir, "indiv" + str(indiv + 1) + ".regions.log")))
def build_fastas_chromosomes(reference, genotypes_for_inds, haploid, output_dir, printer):
printer.out("BUILD FASTA GENOME FOR EACH INDIVIDUAL...\n")
fasta_orig = SeqIO.index(reference, "fasta")
for chrm, svs_infos in genotypes_for_inds.items():
printer.out("PROCESSING CHROMOSOME {0}...\n".format(chrm))
svs = list(svs_infos.keys())
svs = sorted(svs, key=lambda x:_svsort(x, chrm, genotypes_for_inds))
fasta_orig_chr = fasta_orig[chrm]
last_nt = len(fasta_orig_chr)-1
# Compute keeped genomic regions for each diploid chromosome:
regions, current_region_pointer = _compute_keeped_genomic_regions(svs, svs_infos, haploid)
# Build FASTA of each diploid/haploid chromosome:
_build_fastas(chrm, regions, current_region_pointer, output_dir, fasta_orig_chr, last_nt)
def generate_samples_fastq(haploid, nb_inds, output_dir, coverage, read_len, insert_len_mean, insert_len_sd,
prg_path, threads, stdout, stderr):
# Generate reads for all individuals:
cmd = [prg_path + "/pirs/pirs", "simulate", "-z", "-x", str(coverage), "-d", "-B",
prg_path + "/pirs/Profiles/Base-Calling_Profiles/humNew.PE100.matrix.gz", "-I",
prg_path + "/pirs/Profiles/InDel_Profiles/phixv2.InDel.matrix", "-l", str(read_len), "-m",
str(insert_len_mean), "-v", str(insert_len_sd),
"-G", prg_path + "/pirs/Profiles/GC-depth_Profiles/humNew.gcdep_100.dat", "-t", str(threads), "-o"]
if haploid:
cmd.remove("-d")
for i in range(1, nb_inds+1):
cmd_full = cmd + [output_dir, "-s", "indiv%d" % i]
prefix_fasta = os.path.join(output_dir, "indiv" + str(i))
chr0 = prefix_fasta + "_chr_0.fasta"
if not haploid:
chr1 = prefix_fasta + "_chr_1.fasta"
cmd_full += [chr0, chr1]
else:
cmd_full.append(chr0)
subprocess.call(cmd_full, stdout=open(stdout, "a") if stdout is not None else None,
stderr=open(stderr, "a") if stderr is not None else None)
def confirm(deletions: dict, variants: dict, printer: Print):
nb_dels = 0
variants = sorted(variants["DEL"], key=lambda x: x["min"])
variants_counts = OrderedDict()
variants_counts_chr = {}
for variant in variants:
variants_counts["{0}-{1}".format(variant["min"], variant["max"])] = 0
for chrm, deletes in deletions.items():
nb_dels_chr = len(deletes)
nb_dels += nb_dels_chr
variants_counts_chr[chrm] = nb_dels_chr
for delete in deletes:
v_len = delete["length"]
for variant in variants:
if variant["min"] < v_len < variant["max"]:
variants_counts["{0}-{1}".format(variant["min"], variant["max"])] += 1
break
printer.out("We generate {0} deletion variants.".format(nb_dels))
printer.out("Ranges:")
for v_range, v_count in variants_counts.items():
printer.out("\t- Range {0}: {1}".format(v_range, v_count))
printer.out("Chromosomes:")
for chrm in sorted(list(variants_counts_chr.keys())):
printer.out("\t- {0}: {1}".format(chrm, variants_counts_chr[chrm]))
printer.out("")
return input("Continue [Y/n]? ") in ["y", "Y", ""]
def init(output_dir, force_outputdir, sv_list, nstretches, nb_inds, reference, proba_del, haploid, force_polymorphism,
coverage, read_len, insert_len_mean, insert_len_sd, threads, genotypes=None, min_deletions=1, quiet=True,
stdout=None, stderr=None):
printer = Print(stdout=stdout, stderr=stderr)
if os.path.isdir(output_dir):
if force_outputdir:
shutil.rmtree(output_dir)
else:
printer.err("Error: output directory {0} already exists.".format(output_dir))
return 1
elif os.path.isfile(output_dir):
printer.err("Error: unable to create output directory {0}: file exists.".format(output_dir))
return 1
if nb_inds is not None and nb_inds < 2:
printer.err("nb-inds must be at least 2")
return 1
if not os.path.isfile(reference + ".fai"):
os.system("samtools faidx " + reference)
tmp_dir = tempfile.mkdtemp()
prg_path = os.path.dirname(os.path.realpath(__file__))
os.mkdir(output_dir)
############################
# Define fixed files names #
############################
output_vcf = os.path.join(output_dir, "genotypes.vcf")
################
# Launch steps #
################
deletions = None
sv_sim = None
if genotypes is None:
printer.out("GENERATE RANDOM DELETIONS VARIANTS...\n")
try:
nb_deletions = 0
nb_try = 0
sv_sim = VariantsSimulator(sv_list, nstretches, threads, stdout, stderr)
printer.out("Try to generate at least %s deletions..." % min_deletions)
max_try = 10
while nb_deletions < min_deletions and nb_try < max_try:
printer.out("\nTry {0} / {1}...".format(nb_try + 1, max_try))
nb_deletions, deletions = sv_sim.get_random_deletions(proba_del, reference)
sv_sim.print_flush()
nb_try += 1
if nb_deletions < min_deletions:
printer.err("\nUnable to generate %s deletions. Try to reduce size of deletions or increase "
"general probability to have a deletion." % min_deletions)
return 1
printer.out("")
except InputException as e:
printer.err(e)
return 1
except IOError as e:
printer.err(e)
return 1
except Exception:
printer.err(traceback.format_exc())
return 1
if quiet or genotypes is not None or confirm(deletions, sv_sim.variants, printer):
try:
genotypes_for_inds = None
if genotypes is None:
printer.out("GENERATE SUMMARY VCF FILE...\n")
genotypes_for_inds = build_genotypes_vcf_list(deletions, output_vcf, haploid, force_polymorphism, nb_inds,
tmp_dir, prg_path)
else:
nb_inds, genotypes_for_inds = load_genotypes_from_file(genotypes)
if nb_inds < 2:
printer.err("nb-inds must be at least 2")
return 1
build_fastas_chromosomes(reference, genotypes_for_inds, haploid, output_dir, printer)
printer.out("GENERATE RANDOM READS FOR EACH INDIVIDUAL FROM GENOME...\n")
generate_samples_fastq(haploid, nb_inds, output_dir, coverage, read_len, insert_len_mean,
insert_len_sd, prg_path, threads, stdout, stderr)
printer.out("DONE!\n")
except ExecException as e:
printer.err(e)
return 1
except Exception:
printer.err(traceback.format_exc())
return 1
else:
printer.out("Aborted!\n")
return 0
def main():
args = parse_args()
reference = args.reference
sv_list = args.sv_list
nstretches = args.nstretches
output_dir = args.output_directory
haploid = args.haploid
nb_inds = args.nb_inds
force_outputdir = args.force_outputdir
proba_del = args.proba_del
threads = args.threads
force_polymorphism = args.force_polymorphism
coverage = args.coverage
read_len = args.read_len
insert_len_mean = args.insert_len_mean
insert_len_sd = args.insert_len_sd
quiet = args.quiet
min_deletions = args.min_deletions
genotypes = args.genotypes
return init(output_dir, force_outputdir, sv_list, nstretches, nb_inds, reference, proba_del, haploid,
force_polymorphism, coverage, read_len, insert_len_mean, insert_len_sd, threads, genotypes,
min_deletions, quiet)
if __name__ == '__main__':
sys.exit(main())