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 generate_supply_network(
parts_sequences,
already_amplified_fragments,
already_ordered_primers,
assembly_method,
):
"""Build the supply network, return the main station.
See the docs for an overview of the supply network.
Parameters
----------
parts_sequences
A dictionary {part_id: "ATGCGC..."} of the base genetic parts, which will
be considered as available for free.
already_amplified_fragments
A dictionary {fragment_id: "ATGCTGA"} providing sequences of fragments
made for previous assemblies, which will be considered as available for
free.
already_ordered_primers
A dictionary {primer_id: "ATGCTGA"} providing sequences of primers
ordered for previous assemblies, which will be considered as available
for free.
assembly_method
Either "gibson", "golden_gate", or "any_method" (each construct will
then be assembled using any method, with a preference for Golden Gate
Assembly)
"""
# PRIMERS SUPPLIERS
already_ordered_primers_library = dw.PartsLibrary(
name="already_ordered_primers", parts_dict=already_ordered_primers,
)
primers_company = dw.CommercialDnaOffer(
name="oligo_supplier", pricing=dw.FixedCostPricing(1), lead_time=0,
sequence_constraints=(dw.SequenceLengthConstraint(max_length=100),)
)
primers_comparator = dw.DnaSuppliersComparator(
suppliers=[primers_company, already_ordered_primers_library]
)
# STATIONS FOR PARTS EXTENSION VIA PCR
primer_homology_selector = dw.TmSegmentSelector(
min_size=19, max_size=25, min_tm=50, max_tm=70
)
parts_pcr_station = dw.PcrExtractionStation(
name="pcr_part_extension_station",
primers_supplier=primers_comparator,
sequences=parts_sequences,
max_overhang_length=30,
extra_cost=2,
homology_selector=primer_homology_selector,
)
already_amplified_fragments_library = dw.PartsLibrary(
name="already_amplified_fragments",
parts_dict=already_amplified_fragments,
)
fragments_comparator = dw.DnaSuppliersComparator(
name="fragments_comparator",
suppliers=[parts_pcr_station, already_amplified_fragments_library],
)
# ASSEMBLY STATIONS
gibson_assembly_station = dw.DnaAssemblyStation(
name="gibson_assembly",
supplier=fragments_comparator,
assembly_method=dw.GibsonAssemblyMethod(
overhang_selector=dw.FixedSizeSegmentSelector(40),
cost=50
),
coarse_grain=600,
fine_grain=None,
a_star_factor="auto"
)
golden_gate_stations_comparator = dw.DnaSuppliersComparator(
name="golden_gate_comparator",
return_first_accepted_quote=True,
suppliers=[
dw.DnaAssemblyStation(
name="golden_gate_assembly_%s" % enzyme,
supplier=fragments_comparator,
assembly_method=dw.GoldenGateAssemblyMethod(
enzyme=enzyme
),
coarse_grain=600,
fine_grain=None,
cut_spread_radius=2,
a_star_factor="auto"
)
for enzyme in ["BsmBI", "BsaI", "BbsI"]
]
)
# SELECT SUPPLIERS DEPENDING ON THE SELECTED ASSEMBLY METHOD
suppliers = []
if assembly_method in ["golden_gate", "any_method"]:
suppliers.append(golden_gate_stations_comparator)
if assembly_method in ["gibson", "any_method"]:
suppliers.append(gibson_assembly_station)
# RETURN THE METHODS COMPARATOR
main_station = dw.DnaSuppliersComparator(name="main", suppliers=suppliers)
return main_station
import dnaweaver as dw
from dnaweaver.reports import plot_supply_network, AssemblyPlan
import time
cheap_dna_offer = dw.CommercialDnaOffer(
name="CheapDNA.",
sequence_constraints=[
dw.NoPatternConstraint(enzyme="BsaI"),
dw.SequenceLengthConstraint(max_length=4000),
],
pricing=dw.PerBasepairPricing(0.10),
)
oligo_dna_offer = dw.CommercialDnaOffer(
name="OliGoo",
sequence_constraints=[
dw.GcContentConstraint(min_gc=0.3, max_gc=0.7),
dw.SequenceLengthConstraint(max_length=100),
],
pricing=dw.PerBasepairPricing(0.07),
memoize=True,
)
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_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')
import dnaweaver as dw
import matplotlib.pyplot as plt
# 1. DEFINE THE SUPPLY NETWORK (2 VENDORS FEEDING AN ASSEMBLY STATION)
cheap_dna_offer = dw.CommercialDnaOffer(
name="CheapDNA",
sequence_constraints=[
dw.NoPatternConstraint(enzyme="BsmBI"),
dw.SequenceLengthConstraint(max_length=4000),
],
pricing=dw.PerBasepairPricing(0.10),
)
deluxe_dna_offer = dw.CommercialDnaOffer(
name="DeluxeDNA",
sequence_constraints=[dw.SequenceLengthConstraint(max_length=3000)],
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,
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,
)
import os
import dnaweaver as dw
from dnaweaver.biotools import gc_content
import matplotlib.pyplot as plt
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=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,
)
# This example feeds 2 sequences, one with BsmBI sites, the other without, to
# a comparator Gibson/Golden Gate assembly.
# For more realism, the folling adapters as added to the network:
# - A Golden Gate adapter which adds flanks TAGG-ACGA to the sequence for
# assembly on an EMMA plasmid
# - A Gibson Assembly adapter which adds flanks to the sequence for assembly on
# a backbone
# - A linearization station which linearizes parts provided on a backbone by
# the commercial provider Plasmideroo.
import dnaweaver as dw
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(),
import dnaweaver as dw
import os
oligos_company = dw.CommercialDnaOffer(
"OligoCompany",
sequence_constraints=[dw.SequenceLengthConstraint(max_length=200)],
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())
