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 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,
)