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,
logger="bar",
a_star_factor=a_star_factor,
memoize=memoize,
)
with open("50kb_sequence.txt", "r") as f:
sequence = f.read()
print("Generating an assembly plan...")
chunks_assembly_station.prepare_network_on_sequence(sequence)
quote = chunks_assembly_station.get_quote(sequence, with_assembly_plan=True)
print(quote.assembly_step_summary())
print("Generating report...")
assembly_plan_report = quote.to_assembly_plan_report()
assembly_plan_report.write_full_report("report.zip")
print("Done! (see report.zip)")
enzyme="BsmBI"),
supplier=[
company_ingen,
emma_collection,
mouse_pcr_station,
company_tdi,
],
coarse_grain=100,
fine_grain=None,
logger="bar",
)
for station, color in [
(company_ingen, "#fdfdb3"),
(company_oligo, "#b8b6e6"),
(company_tdi, "#c8f8c4"),
(mouse_pcr_station, "#eff5f5"),
(emma_collection, "#f8c3c3"),
]:
station.report_color = color
# LOAD THE SEQUENCE AND PREPARE THE NETWORK FOR IT. HERE THE
# PREPARATION WILL ONLY MAKE THE PCR STATION PRE-BLAST THE SEQUENCE
record = load_record("example_sequence.gb")
assembly_station.prepare_network_on_sequence(record)
quote = assembly_station.get_quote(record, with_assembly_plan=True)
assembly_report = quote.to_assembly_plan_report()
assembly_report.write_full_report("EMMA_assembly_report")
print("Success! See figure assembly_plans.png.")
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