def new(self, root_dir, strains, aligned, sample):
out_dir = root_dir + "/" + sample[0]
os.makedirs(out_dir, exist_ok=True)
# sample_json = out_dir + "/sample.json"
# w.write(sample_json, w.json(s.to_json(sample)))
sample_fasta = out_dir + "/sample.fasta"
w.write(sample_fasta, w.fasta(s.to_fasta(sample)))
art_prefix = out_dir + "/art"
art = os.environ['ART_ILLUMINA']
subprocess.run([
art, "--in", sample_fasta, "--out", art_prefix, "--seqSys", "HS20",
"--len", "100", "--fcov", "100"
],
stdout=subprocess.DEVNULL)
take_ref = False
art_output = r.read(art_prefix + ".aln", r.aln(take_ref))
instance = Instance().new(strains, aligned, art_output)
# w.write(out_dir + "/instance.json", w.json(instance.to_json()))
w.write(out_dir + "/instance.txt", w.text(instance.to_text()))
w.write(out_dir + "/instance.stats.json", w.json(instance.stats()))
class Simulation:
def new(self, params):
os.makedirs(params.out_dir, exist_ok=True)
self.params = params
w.write(params.out_dir + "/params.json",
w.pretty_json(params.to_json()))
self.sample = Sample().new(params)
sample_file = params.out_dir + "/sample.fasta"
w.write(sample_file, w.fasta(self.sample))
art_prefix = params.out_dir + "/art"
art = os.environ['ART_ILLUMINA']
subprocess.run([
art, "--in", sample_file, "--out", art_prefix, "--rndSeed",
str(params.seed)
] + params.art_flags,
stdout=subprocess.DEVNULL)
self.art_output = r.read(art_prefix + ".aln", r.aln(params.take_ref))
self.instance = Instance().new(params, self.art_output)
w.write(params.out_dir + "/instance.json",
w.json(self.instance.to_json()))
w.write(params.out_dir + "/instance.txt",
w.text(self.instance.to_text()))
w.write(params.out_dir + "/instance.stats.json",
w.json(self.instance.stats()))
return self
def load(self, out_dir):
self.params = Params().from_json(
r.read(out_dir + "/params.json", r.json))
self.sample = Sample().from_fasta(
r.read(out_dir + "/sample.fasta", r.fasta_list))
self.art_output = r.read(out_dir + "/art.aln",
r.aln(self.params.take_ref))
self.instance = Instance().from_json(
r.read(out_dir + "/instance.json", r.json))
return self
