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