def test_emma_construct():
emma_collection = GoldenGatePartsLibrary("EMMA",
fasta_file=EMMA_PATH,
memoize=True)
company_ingen = CommercialDnaOffer(
name="InGen",
pricing=PerBasepairPricing(0.14),
sequence_constraints=[SequenceLengthConstraint(max_length=2400)])
company_tdi = CommercialDnaOffer(
name="TDI",
pricing=PerBasepairPricing(0.08),
sequence_constraints=[SequenceLengthConstraint(max_length=600)])
assembly_station = DnaAssemblyStation(
name='GoldenGate Assembly Station',
assembly_method=GoldenGateAssemblyMethod(
min_segment_length=40,
max_segment_length=5000,
enzyme='BsmBI',
# max_fragments=8
),
supplier=[company_ingen, emma_collection, company_tdi],
coarse_grain=100,
fine_grain=10,
logger='bar',
a_star_factor='auto')
record = load_record(SEQUENCE_PATH)
sequence = str(record.seq)
quote = assembly_station.get_quote(sequence, with_assembly_plan=True)
emma_parts = [
p for p in list(quote.assembly_plan.values())
if p.source.name == 'EMMA'
]
assert len(emma_parts) == 6
def test_circular_gibson():
record = dw.load_record(plasmid_path)
sequence = dw.SequenceString.from_record(record)
assert sequence.metadata['topology'] == "circular"
assert dw.get_sequence_topology(sequence) == "circular"
commercial_provider = dw.CommercialDnaOffer(
name="supplier", pricing=dw.PerBasepairPricing(0.1),
)
assembly_station = dw.DnaAssemblyStation(
name="golden_gate",
supplier=commercial_provider,
assembly_method=dw.GibsonAssemblyMethod(
overhang_selector=dw.TmSegmentSelector(),
max_segment_length=3000
),
coarse_grain=600,
fine_grain=None,
cut_spread_radius=2,
)
quote = assembly_station.get_quote(sequence)
assert quote.accepted
assert 1200 < quote.price < 1220
# ROUND TRIP: SIMULATE CLONING TO CHECK ASSEMBLY PLAN VALIDITY
part_names, repo = extract_records_from_quote(quote)
quote = assembly_station.get_quote(sequence)
assembly = dc.GibsonAssembly(parts=part_names)
simulation = assembly.simulate(repo)
assert len(simulation.construct_records) == 1
simulated_record = simulation.construct_records[0]
print (len(record), len(simulated_record))
assert sequences_are_circularly_equal([record, simulated_record])
def test_example_with_adapters():
oligo_com = dw.CommercialDnaOffer(
name="Oligo.com",
sequence_constraints=[dw.SequenceLengthConstraint(max_length=200)],
pricing=dw.PerBasepairPricing(0.10),
lead_time=7,
)
plasmideroo = dw.CommercialDnaOffer(
name="Plasmideroo",
sequence_constraints=[dw.SequenceLengthConstraint(max_length=4000)],
pricing=dw.PerBasepairPricing(0.20),
lead_time=10,
)
plasmideroo_linearization = dw.PcrLinearizationStation(
name="Gibson Linearization",
supplier=plasmideroo,
primers_supplier=oligo_com,
homology_selector=dw.TmSegmentSelector(),
)
gibson_blocks_assembly_station = dw.DnaAssemblyStation(
name="Gibson Assembly",
assembly_method=dw.GibsonAssemblyMethod(
overhang_selector=dw.FixedSizeSegmentSelector(80),
min_segment_length=1000,
max_segment_length=4000,
duration=8,
cost=16,
),
supplier=plasmideroo_linearization,
coarse_grain=100,
fine_grain=False,
a_star_factor="auto",
)
gibson_station_adapter = dw.SequenceAdapter(
name="Gibson Adapter",
supplier=gibson_blocks_assembly_station,
left_addition="TAAGACTAGTGCACATAATACGG",
right_addition="ATTGTCACACTACAAACATGAC",
)
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=plasmideroo,
coarse_grain=100,
fine_grain=False,
a_star_factor="auto",
)
golden_gate_station_adapter = dw.SequenceAdapter(
name="Golden Gate Adapter",
supplier=goldengate_blocks_assembly_station,
left_addition="TAGG",
right_addition="ACGA",
)
main_source = dw.DnaSuppliersComparator(
[gibson_station_adapter, golden_gate_station_adapter]
)
# RESOLUTION
print("\n\nSEQUENCE WITHOUT BMSBI SITES:\n")
path = os.path.join(this_directory, "sequence_no_bsmbi.fa")
sequence = dw.load_record(path)
quote = main_source.get_quote(sequence, with_assembly_plan=True)
assert quote.source == goldengate_blocks_assembly_station
print(quote.assembly_step_summary())
assert 2000 < quote.price < 2020
print("\n\nSEQUENCE WITH BMSBI SITES:\n")
path = os.path.join(this_directory, "sequence_bsmbi.fa")
sequence = dw.load_record(path)
quote = main_source.get_quote(sequence, with_assembly_plan=True)
print(quote.assembly_step_summary())
assert quote.source == gibson_blocks_assembly_station
assert 2050 < quote.price < 2100
# FOR COVERAGE
assembly_report = quote.to_assembly_plan_report()
assembly_report.write_full_report('@memory')
pricing=dw.PerBasepairPricing(0.20),
)
assembly_station = dw.DnaAssemblyStation(
name="Gibson Assembly Station",
assembly_method=dw.GibsonAssemblyMethod(
overhang_selector=dw.TmSegmentSelector(min_tm=55, max_tm=70),
min_segment_length=500,
max_segment_length=4000,
),
supplier=[cheap_dna_offer, deluxe_dna_offer],
logger="bar",
coarse_grain=20,
fine_grain=1,
)
# 2. FIND AN ASSEMBLY PLAN AND CREATE A REPORT.
sequence = dw.load_record("sequence_with_bsmbi_sites.fa")
quote = assembly_station.get_quote(sequence, with_assembly_plan=True)
print(quote.assembly_step_summary())
assembly_report = quote.to_assembly_plan_report()
_, ax = assembly_report.plot_supply_network()
ax.figure.savefig("supply_network_2_vendors.pdf", bbox_inches="tight")
figure, ax = plt.subplots(1, figsize=(7, 3))
assembly_report.plot_assembly_blocks(ax=ax,
parts_offset=0.1,
plot_top_assembly=False,
legend=True)
figure.savefig("fragments_from_2_vendors.pdf", bbox_inches="tight")
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.")
fine_grain=False,
a_star_factor="auto")
golden_gate_station_adapter = dw.SequenceAdapter(
name="Golden Gate Adapter",
supplier=goldengate_blocks_assembly_station,
left_addition="TAGG",
right_addition="ACGA",
)
main_source = dw.DnaSuppliersComparator(
[gibson_station_adapter, golden_gate_station_adapter])
# RESOLUTION
print("\n\nSEQUENCE WITHOUT BMSBI SITES:\n")
sequence = dw.load_record("sequence_no_bsmbi.fa")
quote = main_source.get_quote(sequence, with_assembly_plan=True)
print(quote.assembly_step_summary())
print("\n\nSEQUENCE WITH BMSBI SITES:\n")
sequence = dw.load_record("sequence_bsmbi.fa")
quote = main_source.get_quote(sequence, with_assembly_plan=True)
print(quote.assembly_step_summary())
# PLOT THE SUPPLY GRAPH
assembly_report = quote.to_assembly_plan_report()
_, ax = assembly_report.plot_supply_network()
ax.figure.savefig("supply_network.pdf", bbox_inches="tight")
pricing=dw.PerBasepairPricing(0.1))
ecoli_db_path = os.path.join('..', '..', 'data', 'ecoli_blast_db', 'ecoli')
pcr_station = dw.PcrExtractionStation(name="PCR station",
max_overhang_length=50,
homology_selector=dw.TmSegmentSelector(),
primers_supplier=oligos_company,
blast_database=ecoli_db_path,
extra_cost=5)
assembly_station = dw.DnaAssemblyStation(
name="Golden Gate assembly",
assembly_method=dw.GoldenGateAssemblyMethod(enzyme='BsaI'),
supplier=pcr_station,
coarse_grain=100,
fine_grain=0,
logger='bar')
# LOAD THE (SITE-FREE) DESIRED SEQUENCE
desired_sequence = str(dw.load_record("desired_sequence.gb").seq)
# THIS LINE WILL PRE-BLAST THE SEQUENCE TO ACCELERATE COMPUTATIONS.
assembly_station.prepare_network_on_sequence(desired_sequence)
# FIND AN ASSEMBLY PLAN AND PRINT IT.
quote = assembly_station.get_quote(desired_sequence, with_assembly_plan=True)
print(quote.assembly_step_summary())
quote.compute_fragments_final_locations()
report = quote.to_assembly_plan_report()
report.write_full_report("report.zip")
print("Done! (see report.zip)")
import os
import dnaweaver as dw
import json
ecoli_db_path = os.path.join("..", "..", "data", "ecoli_blast_db", "ecoli")
dw.PcrExtractionStation.dna_banks = {"e_coli": ecoli_db_path}
dw.PartsLibrary.collections_by_id["EMMA"] = dict(library_class="golden_gate",
fasta_file="emma_parts.fa")
sequence = dw.load_record("sequence_with_emma_and_ecoli_parts.fa")
main_station = dw.DnaSupplier.from_json_data("state_from_web_app.json")
main_station.prepare_network_on_sequence(sequence)
quote = main_station.get_quote(sequence)
print(quote.assembly_step_summary())