def make(self) -> None:
self.genome = GenomeLibrary()
self.genome.make(bg_size=300,
bg_gc_content=0.45,
bg_rnd=self.make_generator())
self.genome.bind(host=self)
self.genexpr = GenomeExpression()
self.genexpr.make(
opt_primer_len=20,
infl_prom_str=40,
species_prom_str=0.057,
regressor_file=DATADIR / 'expression_predictor' /
'Ecol-Promoter-predictor.pkl',
addparams_file=DATADIR / 'expression_predictor' /
'Ecol-Promoter-AddParams.pkl',
)
self.genexpr.bind(host=self, genome=self.genome)
path = DATADIR / 'metabolic_model' / 'e_coli_core.xml'
model = cobra.io.read_sbml_model(str(path))
self.metflux = MetabolicFlux()
self.metflux.make(model=model)
self.metflux.bind(host=self)
def make(self, opt_growth_temp: int, max_biomass: int, infl_prom_str: int,
species_prom_str: int, opt_primer_len: int, regressor_file: Path,
addparams_file: Path) -> None:
if not alldef(opt_growth_temp, max_biomass, infl_prom_str,
species_prom_str, opt_primer_len, regressor_file,
addparams_file):
raise HostException(
"Host not initialized. Reason: incomplete arguments.")
# Setup GenomeList module
self.genome = GenomeList()
self.genome.make()
self.genome.bind(host=self)
# Setup GenomeExpression module
self.genexpr = GenomeExpression()
self.genexpr.make(opt_primer_len=opt_primer_len,
infl_prom_str=infl_prom_str,
species_prom_str=species_prom_str,
regressor_file=regressor_file,
addparams_file=addparams_file)
self.genexpr.bind(host=self, genome=self.genome)
# Setup GrowthBehaviour module
self.growth = GrowthBehaviour()
self.growth.make(opt_growth_temp=opt_growth_temp,
max_biomass=max_biomass)
self.growth.bind(host=self, genexpr=self.genexpr)
def copy(self, ref: 'EcolFluxHost') -> None:
self.genome = GenomeLibrary()
self.genome.copy(ref=ref.genome)
self.genome.bind(host=self)
self.genexpr = GenomeExpression()
self.genexpr.copy(ref=ref.genexpr)
self.genexpr.bind(host=self, genome=self.genome)
self.metflux = MetabolicFlux()
self.metflux.copy(ref=ref.metflux)
self.metflux.bind(host=self)
class EcolFluxHost(Host):
genome: GenomeLibrary
genexpr: GenomeExpression
metflux: MetabolicFlux
def make(self) -> None:
self.genome = GenomeLibrary()
self.genome.make(bg_size=300,
bg_gc_content=0.45,
bg_rnd=self.make_generator())
self.genome.bind(host=self)
self.genexpr = GenomeExpression()
self.genexpr.make(
opt_primer_len=20,
infl_prom_str=40,
species_prom_str=0.057,
regressor_file=DATADIR / 'expression_predictor' /
'Ecol-Promoter-predictor.pkl',
addparams_file=DATADIR / 'expression_predictor' /
'Ecol-Promoter-AddParams.pkl',
)
self.genexpr.bind(host=self, genome=self.genome)
path = DATADIR / 'metabolic_model' / 'e_coli_core.xml'
model = cobra.io.read_sbml_model(str(path))
self.metflux = MetabolicFlux()
self.metflux.make(model=model)
self.metflux.bind(host=self)
def copy(self, ref: 'EcolFluxHost') -> None:
self.genome = GenomeLibrary()
self.genome.copy(ref=ref.genome)
self.genome.bind(host=self)
self.genexpr = GenomeExpression()
self.genexpr.copy(ref=ref.genexpr)
self.genexpr.bind(host=self, genome=self.genome)
self.metflux = MetabolicFlux()
self.metflux.copy(ref=ref.metflux)
self.metflux.bind(host=self)
def sync(self) -> None:
self.sync_modules([self.genome, self.genexpr, self.metflux])
def edit_gene(self, gene_name: str, new_promoter: Seq) -> None:
found_genes = [
gene for gene in self.genome.locgenes if gene_name == gene.name
]
if len(found_genes) > 0:
self.emit(AlterGenePromoterEvent(found_genes[0], new_promoter))
def optimize(self) -> CobraSolution:
return self.metflux.optimize()
def copy(self, ref: RecHost) -> None:
# Setup GenomeList module using the ref
self.genome = GenomeList()
self.genome.copy(ref=ref.genome)
self.genome.bind(host=self)
# Setup GenomeExpression module using the ref
self.genexpr = GenomeExpression()
self.genexpr.copy(ref=ref.genexpr)
self.genexpr.bind(host=self, genome=self.genome)
# Setup GrowthBehaviour module using the ref
self.growth = GrowthBehaviour()
self.growth.copy(ref=ref.growth)
self.growth.bind(host=self, genexpr=self.genexpr)
class RecHost(Host):
growth: GrowthBehaviour
genome: GenomeList
genexpr: GenomeExpression
ref_prom: str = 'GCCCATTGACAAGGCTCTCGCGGCCAGGTATAATTGCACG'
def make(self, opt_growth_temp: int, max_biomass: int, infl_prom_str: int,
species_prom_str: int, opt_primer_len: int, regressor_file: Path,
addparams_file: Path) -> None:
if not alldef(opt_growth_temp, max_biomass, infl_prom_str,
species_prom_str, opt_primer_len, regressor_file,
addparams_file):
raise HostException(
"Host not initialized. Reason: incomplete arguments.")
# Setup GenomeList module
self.genome = GenomeList()
self.genome.make()
self.genome.bind(host=self)
# Setup GenomeExpression module
self.genexpr = GenomeExpression()
self.genexpr.make(opt_primer_len=opt_primer_len,
infl_prom_str=infl_prom_str,
species_prom_str=species_prom_str,
regressor_file=regressor_file,
addparams_file=addparams_file)
self.genexpr.bind(host=self, genome=self.genome)
# Setup GrowthBehaviour module
self.growth = GrowthBehaviour()
self.growth.make(opt_growth_temp=opt_growth_temp,
max_biomass=max_biomass)
self.growth.bind(host=self, genexpr=self.genexpr)
def copy(self, ref: RecHost) -> None:
# Setup GenomeList module using the ref
self.genome = GenomeList()
self.genome.copy(ref=ref.genome)
self.genome.bind(host=self)
# Setup GenomeExpression module using the ref
self.genexpr = GenomeExpression()
self.genexpr.copy(ref=ref.genexpr)
self.genexpr.bind(host=self, genome=self.genome)
# Setup GrowthBehaviour module using the ref
self.growth = GrowthBehaviour()
self.growth.copy(ref=ref.growth)
self.growth.bind(host=self, genexpr=self.genexpr)
def sync(self) -> None:
self.sync_modules([self.genome, self.genexpr, self.growth])
def find_gene_or_abort(self, gene_name: str) -> Gene:
"""
Find a gene by a given name or abort with an exception.
Throws: HostException
"""
gene: Optional[Gene] = first(self.genome.genes,
lambda g: g.name == gene_name)
# Find the first gene matching the name.
if gene is None:
raise HostException(
"Host has not found the gene '{}'".format(gene_name))
return gene
def insert_gene(self, gene: Gene) -> None:
self.emit(InsertGeneEvent(gene=gene, locus=0))
def print_status(self) -> None:
print("Host [{}]:".format(self.name))
print(" seed plus counter = {} + {}".format(self.rnd_seed,
self.rnd_counter))
print(" optimal growth temperature = {}".format(
self.growth.opt_growth_temp))
print(" max biomass = {}".format(self.growth.max_biomass))
print(" optimal primer length = {}".format(
self.genexpr.opt_primer_len))
print(" Gene List: {} genes".format(len(self.genome.genes)))
for gene in self.genome.genes:
print(" - {} = {} * {}".format(gene.name, gene.prom, gene.orf))
print(" Event History: {} events".format(len(self.event_log)))
for el in self.event_log:
print(" - {}".format(el))