three-step_assembly.py

import os
from dnaweaver import (
    PcrExtractionStation,
    CommercialDnaOffer,
    DnaAssemblyStation,
    GibsonAssemblyMethod,
    GoldenGateAssemblyMethod,
    OligoAssemblyMethod,
    DnaSuppliersComparator,
    TmSegmentSelector,
    FixedSizeSegmentSelector,
    PerBasepairPricing,
    NoPatternConstraint,
    SequenceLengthConstraint,
)
from dnaweaver.biotools import gc_content


a_star_factor = "auto"
# a_star_factor = 0
memoize = True

# OLIGO COMPANIES

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_db_path = os.path.join("..", "..", "data", "ecoli_blast_db", "ecoli")
ecoli_genome = PcrExtractionStation(
    "E. coli Genome (PCR)",
    primers_supplier=oligo_com,
    blast_database=ecoli_db_path,
    homology_selector=TmSegmentSelector(),
    max_amplicon_length=10000,
    extra_time=3,
    extra_cost=1,
)


# CHUNKS TO MEGACHUNKS ASSEMBLY

chunks_assembly_station = DnaAssemblyStation(
    name="Chunks assembly (Yeast)",
    assembly_method=GibsonAssemblyMethod(
        overhang_selector=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,
    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)")