def generate_supply_network(a_star_factor):
oligo_com = dw.CommercialDnaOffer(
name="Oligo.com",
sequence_constraints=[dw.SequenceLengthConstraint(max_length=200)],
pricing=dw.PerBasepairPricing(0.10),
lead_time=7,
)
deluxe_dna_com = dw.CommercialDnaOffer(
name="DeluxeDNA.com",
sequence_constraints=[dw.SequenceLengthConstraint(max_length=4000)],
pricing=dw.PerBasepairPricing(0.20),
lead_time=10,
)
cheap_dna_com = dw.CommercialDnaOffer(
name="CheapDNA.com",
sequence_constraints=[
dw.SequenceLengthConstraint(max_length=4000),
dw.NoPatternConstraint(enzyme="AarI"),
dw.NoPatternConstraint(enzyme="BsaI"),
lambda seq: (0.4 < gc_content(seq) < 0.6),
],
pricing=dw.PerBasepairPricing(0.10),
lead_time=15,
)
# OLIGOS TO BLOCKS ASSEMBLY
oligo_assembly_station = dw.DnaAssemblyStation(
name="Oligo Assembly Station",
assembly_method=dw.OligoAssemblyMethod(
overhang_selector=dw.TmSegmentSelector(
min_size=15, max_size=25, min_tm=50, max_tm=70
),
min_segment_length=40,
max_segment_length=200,
sequence_constraints=[dw.SequenceLengthConstraint(max_length=1500)],
duration=8,
cost=2,
),
supplier=oligo_com,
coarse_grain=20,
fine_grain=False,
a_star_factor=a_star_factor,
)
# BLOCKS TO CHUNKS ASSEMBLY
blocks_sources_comparator = dw.DnaSuppliersComparator(
name="bs_comparator",
suppliers=[oligo_assembly_station, cheap_dna_com, deluxe_dna_com],
memoize=True,
)
gibson_blocks_assembly_station = dw.DnaAssemblyStation(
name="Gibson Blocks Assembly",
assembly_method=dw.GibsonAssemblyMethod(
overhang_selector=dw.FixedSizeSegmentSelector(80),
min_segment_length=1000,
max_segment_length=4000,
duration=8,
cost=16,
),
supplier=blocks_sources_comparator,
coarse_grain=300,
fine_grain=False,
memoize=True,
a_star_factor=a_star_factor,
)
goldengate_blocks_assembly_station = dw.DnaAssemblyStation(
name="Golden Gate Blocks Assembly",
assembly_method=dw.GoldenGateAssemblyMethod(
enzyme="BsmBI",
wildcard_basepair="A",
min_segment_length=1000,
max_segment_length=4000,
duration=5,
cost=6,
),
supplier=blocks_sources_comparator,
coarse_grain=400,
fine_grain=False,
memoize=True,
a_star_factor=a_star_factor,
)
ecoli_genome_path = os.path.join(
"..", "..", "data", "ecoli_blast_db", "ecoli"
)
ecoli_genome = dw.PcrExtractionStation(
"E. coli Genome (PCR)",
primers_supplier=oligo_com,
homology_selector=dw.TmSegmentSelector(),
blast_database=ecoli_genome_path,
max_amplicon_length=10000,
extra_time=3,
extra_cost=1,
)
# CHUNKS TO MEGACHUNKS ASSEMBLY
return dw.DnaAssemblyStation(
name="Chunks assembly (Yeast)",
assembly_method=dw.GibsonAssemblyMethod(
overhang_selector=dw.FixedSizeSegmentSelector(300),
min_segment_length=7000,
max_segment_length=25000,
duration=8,
),
supplier=[
ecoli_genome,
goldengate_blocks_assembly_station,
gibson_blocks_assembly_station,
],
coarse_grain=1000,
fine_grain=None,
a_star_factor=a_star_factor,
memoize=True,
)
)
deluxe_dna_com = dw.CommercialDnaOffer(
name="DeluxeDNA.com",
sequence_constraints=[dw.SequenceLengthConstraint(max_length=10000)],
pricing=dw.PerBasepairPricing(0.25),
lead_time=7,
)
cheap_dna_com = dw.CommercialDnaOffer(
name="CheapDNA.com",
sequence_constraints=[
dw.SequenceLengthConstraint(max_length=4000),
dw.NoPatternConstraint(enzyme="AarI"),
dw.NoPatternConstraint(enzyme="BsaI"),
lambda seq: (0.4 < gc_content(seq) < 0.6),
],
pricing=dw.PerBasepairPricing(0.10),
lead_time=15,
)
# OLIGOS TO BLOCKS ASSEMBLY
oligo_assembly_station = dw.DnaAssemblyStation(
name="Oligo Assembly Station",
assembly_method=dw.OligoAssemblyMethod(
overhang_selector=dw.TmSegmentSelector(min_size=15,
max_size=25,
min_tm=50,
max_tm=70),
min_segment_length=40,
def test_full_report():
# OLIGO COMPANIES
a_star_factor = 'auto'
memoize = True
oligo_com = CommercialDnaOffer(
name="Oligo.com",
sequence_constraints=[SequenceLengthConstraint(max_length=200)],
pricing=PerBasepairPricing(0.10),
lead_time=7
)
deluxe_dna_com = CommercialDnaOffer(
name="DeluxeDNA.com",
sequence_constraints=[SequenceLengthConstraint(max_length=4000)],
pricing=PerBasepairPricing(0.20),
lead_time=10
)
cheap_dna_com = CommercialDnaOffer(
name="CheapDNA.com",
sequence_constraints=[SequenceLengthConstraint(max_length=4000),
NoPatternConstraint(enzyme='AarI'),
NoPatternConstraint(enzyme='BsaI'),
lambda seq: (0.4 < gc_content(seq) < 0.6)
],
pricing=PerBasepairPricing(0.10),
lead_time=15
)
# OLIGOS TO BLOCKS ASSEMBLY
oligo_assembly_station = DnaAssemblyStation(
name="Oligo Assembly Station",
assembly_method=BuildAGenomeAssemblyMethod(
overhang_selector=TmOverhangSelector(
min_size=15, max_size=25, min_tm=50, max_tm=70),
min_segment_length=40,
max_segment_length=200,
sequence_constraints=[SequenceLengthConstraint(max_length=1500)],
duration=8,
cost=2
),
dna_source=oligo_com,
coarse_grain=20,
fine_grain=False,
a_star_factor=a_star_factor
)
# BLOCKS TO CHUNKS ASSEMBLY
blocks_sources_comparator = DnaSourcesComparator(
name='bs_comparator',
suppliers=[
oligo_assembly_station,
cheap_dna_com,
deluxe_dna_com
],
memoize=memoize
)
gibson_blocks_assembly_station = DnaAssemblyStation(
name="Gibson Blocks Assembly",
assembly_method=GibsonAssemblyMethod(
overhang_selector=FixedSizeOverhangSelector(80),
min_segment_length=1000,
max_segment_length=4000,
duration=8,
cost=16
),
dna_source=blocks_sources_comparator,
coarse_grain=300,
fine_grain=False,
memoize=memoize,
a_star_factor=a_star_factor
)
goldengate_blocks_assembly_station = DnaAssemblyStation(
name="Golden Gate Blocks Assembly",
assembly_method=GoldenGateAssemblyMethod(
enzyme='BsmBI',
wildcard_basepair="A",
min_segment_length=1000,
max_segment_length=4000,
duration=5,
cost=6
),
dna_source=blocks_sources_comparator,
coarse_grain=400,
fine_grain=False,
memoize=memoize,
a_star_factor=a_star_factor
)
ecoli_genome = PcrOutStation(
"E. coli Genome (PCR)",
primers_dna_source=oligo_com,
blast_database=ECOLI_DB_PATH,
max_amplicon_length=10000,
extra_time=3,
extra_cost=1
)
# CHUNKS TO MEGACHUNKS ASSEMBLY
chunks_assembly_station = DnaAssemblyStation(
name="Chunks assembly (Gibson)",
assembly_method=GibsonAssemblyMethod(
overhang_selector=FixedSizeOverhangSelector(300),
min_segment_length=7000,
max_segment_length=25000,
duration=8
),
dna_source=DnaSourcesComparator([
ecoli_genome,
goldengate_blocks_assembly_station,
gibson_blocks_assembly_station,
]),
coarse_grain=1000,
fine_grain=None,
logger='bars',
a_star_factor=a_star_factor,
memoize=memoize
)
with open(SEQUENCE_PATH, "r") as f:
sequence = f.read()
import time
t0 = time.time()
ecoli_genome.pre_blast(sequence)
quote = chunks_assembly_station.get_quote(
sequence, with_assembly_plan=True)
t1 = time.time()
print("ELAPSED:", "%.02f" % (t1 - t0))
print(quote)
if quote.accepted:
print(quote.assembly_step_summary())
assert (3500 < quote.price < 3600)
quote.compute_full_assembly_tree()
quote.compute_fragments_final_locations()
json_quote = JsonQuote.from_dnaweaver_quote(quote)
autocolor_quote_sources(json_quote)
data = make_folder_report(json_quote, '@memory')
def test_lead_time_limit():
# OLIGO COMPANIES
a_star_factor = "auto"
memoize = True
oligo_com = CommercialDnaOffer(
name="Oligo.com",
sequence_constraints=[SequenceLengthConstraint(max_length=200)],
pricing=PerBasepairPricing(0.10),
lead_time=7,
)
deluxe_dna_com = CommercialDnaOffer(
name="DeluxeDNA.com",
sequence_constraints=[SequenceLengthConstraint(max_length=4000)],
pricing=PerBasepairPricing(0.20),
lead_time=10,
)
cheap_dna_com = CommercialDnaOffer(
name="CheapDNA.com",
sequence_constraints=[
SequenceLengthConstraint(max_length=4000),
NoPatternConstraint(enzyme="AarI"),
NoPatternConstraint(enzyme="BsaI"),
lambda seq: (0.4 < gc_content(seq) < 0.6),
],
pricing=PerBasepairPricing(0.10),
lead_time=15,
)
# OLIGOS TO BLOCKS ASSEMBLY
oligo_assembly_station = DnaAssemblyStation(
name="Oligo Assembly Station",
assembly_method=OligoAssemblyMethod(
overhang_selector=TmSegmentSelector(min_size=15,
max_size=25,
min_tm=50,
max_tm=70),
min_segment_length=40,
max_segment_length=200,
sequence_constraints=[SequenceLengthConstraint(max_length=1500)],
duration=8,
cost=2,
),
supplier=oligo_com,
coarse_grain=20,
fine_grain=False,
a_star_factor=a_star_factor,
)
# BLOCKS TO CHUNKS ASSEMBLY
blocks_sources_comparator = DnaSuppliersComparator(
name="bs_comparator",
suppliers=[oligo_assembly_station, cheap_dna_com, deluxe_dna_com],
memoize=memoize,
)
gibson_blocks_assembly_station = DnaAssemblyStation(
name="Gibson Blocks Assembly",
assembly_method=GibsonAssemblyMethod(
overhang_selector=FixedSizeSegmentSelector(80),
min_segment_length=1000,
max_segment_length=4000,
duration=8,
cost=16,
),
supplier=blocks_sources_comparator,
coarse_grain=300,
fine_grain=False,
memoize=memoize,
a_star_factor=a_star_factor,
)
goldengate_blocks_assembly_station = DnaAssemblyStation(
name="Golden Gate Blocks Assembly",
assembly_method=GoldenGateAssemblyMethod(
enzyme="BsmBI",
wildcard_basepair="A",
min_segment_length=1000,
max_segment_length=4000,
duration=5,
cost=6,
),
supplier=blocks_sources_comparator,
coarse_grain=400,
fine_grain=False,
memoize=memoize,
a_star_factor=a_star_factor,
)
ecoli_genome = PcrExtractionStation(
"E. coli Genome (PCR)",
primers_supplier=oligo_com,
homology_selector=TmSegmentSelector(min_size=18,
max_size=22,
min_tm=55,
max_tm=65),
blast_database=ECOLI_DB_PATH,
max_amplicon_length=10000,
extra_time=3,
extra_cost=1,
)
# CHUNKS TO MEGACHUNKS ASSEMBLY
chunks_assembly_station = DnaAssemblyStation(
name="Chunks assembly (Gibson)",
assembly_method=GibsonAssemblyMethod(
overhang_selector=FixedSizeSegmentSelector(300),
min_segment_length=7000,
max_segment_length=25000,
duration=8,
),
supplier=DnaSuppliersComparator([
ecoli_genome,
goldengate_blocks_assembly_station,
gibson_blocks_assembly_station,
]),
coarse_grain=1000,
fine_grain=None,
a_star_factor=a_star_factor,
memoize=memoize,
)
with open(SEQUENCE_PATH, "r") as f:
sequence = f.read()
import time
t0 = time.time()
chunks_assembly_station.prepare_network_on_sequence(sequence)
quote = chunks_assembly_station.get_quote(sequence,
max_lead_time=28,
with_assembly_plan=True)
t1 = time.time()
print("ELAPSED:", "%.02f" % (t1 - t0))
print(quote)
if quote.accepted:
print(quote.assembly_step_summary())
assert 5540 < quote.price < 5550