def test_circular_golden_gate():
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.GoldenGateAssemblyMethod(
enzyme="BsmBI",
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.Type2sRestrictionAssembly(parts=part_names)
simulation = assembly.simulate(repo)
assert len(simulation.construct_records) == 1
simulated_record = simulation.construct_records[0]
assert sequences_are_circularly_equal([record, simulated_record])
def test_autoselect_connectors():
repo = dc.SequenceRepository()
repo.import_records(
collection="parts",
folder=os.path.join(this_directory, "parts"),
use_file_names_as_ids=True,
topology="circular"
)
repo.import_records(
collection="emma_connectors",
folder=os.path.join(this_directory, "emma_connectors"),
use_file_names_as_ids=True,
)
all_parts = list(repo.collections["parts"].keys())
assembly = dc.Type2sRestrictionAssembly(
parts=all_parts, connectors_collection="emma_connectors"
)
simulation = assembly.simulate(sequence_repository=repo)
assert len(simulation.construct_records) == 1
assert len(simulation.warnings) == 1
warning = simulation.warnings[0]
# selected_connectors = mix.autoselect_connectors(connectors)
assert sorted(warning.data["selected_connectors"]) == [
"conn_A_B",
"conn_D-F",
"conn_J-K",
"conn_L-N",
"conn_R-W",
"conn_W-Z",
]
def test_combinatorial_type2s():
repository = dc.SequenceRepository()
repository.import_records(folder=parts_folder, use_file_names_as_ids=True)
parts_list = list(repository.collections["parts"])
# EXPECT A SINGLE CONSTRUCT, GET AN ERROR
assembly = dc.Type2sRestrictionAssembly(parts_list, expected_constructs=1)
simulation = assembly.simulate(sequence_repository=repository)
assert len(simulation.errors) == 1
assert len(simulation.construct_records) == 5
# DON'T EXPECT A CERTAIN NUMBER, GET NO ERROR
assembly = dc.Type2sRestrictionAssembly(parts_list,
expected_constructs="any_number")
simulation = assembly.simulate(sequence_repository=repository)
assert len(simulation.errors) == 0
assert len(simulation.construct_records) == 5
# LIMIT THE NUMBER OF CONSTRUCTS, GET LESS CONSTRUCTS, AND A WARNING
assembly = dc.Type2sRestrictionAssembly(
parts_list,
max_constructs=3,
expected_constructs="any_number",
expect_no_unused_parts=False,
)
simulation = assembly.simulate(sequence_repository=repository)
assert len(simulation.errors) == 0
assert len(simulation.warnings) == 1 # Max constructs reached warning
assert len(simulation.construct_records) == 3
# TEST RANDOMIZED ASSEMBLY PICKING
assembly = dc.Type2sRestrictionAssembly(
parts_list,
max_constructs=2,
expected_constructs="any_number",
expect_no_unused_parts=False,
randomize_constructs=True,
)
simulation = assembly.simulate(sequence_repository=repository)
assert len(simulation.errors) == 0
assert len(simulation.warnings) == 1 # Max constructs reached warning
assert len(simulation.construct_records) == 2
import dnacauldron as dc
import os
repository = dc.SequenceRepository()
repository.import_records(folder="parts", use_file_names_as_ids=True)
parts_list = list(repository.collections["parts"])
assembly = dc.Type2sRestrictionAssembly(
name="randomized_combinatorial_asm",
parts=parts_list,
expected_constructs="any_number",
randomize_constructs=True,
max_constructs=2,
)
simulation = assembly.simulate(sequence_repository=repository, )
output_path = os.path.join("output", "randomized_combinatorial")
simulation.write_report(target=output_path)
print("Done! see output/randomized_combinatorial folder for the results.")
def work(self):
self.logger(message="Reading the Data...")
data = self.data
# CHANGE THE VALUE OF THE BOOLEANS
def yes_no(value):
return {"yes": True, "no": False}.get(value, value)
include_fragment_plots = yes_no(data.include_fragment_plots)
include_graph_plots = yes_no(data.include_graph_plots)
include_assembly_plots = yes_no(data.include_assembly_plots)
report_writer = dc.AssemblyReportWriter(
include_mix_graphs=include_graph_plots,
include_assembly_plots=include_assembly_plots,
include_fragment_plots=include_fragment_plots,
)
# INITIALIZE ALL RECORDS IN A SEQUENCE REPOSITORY
records = records_from_data_files(
data.parts, use_file_names_as_ids=data.use_file_names_as_ids)
repository = dc.SequenceRepository()
for record in records:
# location-less features can cause bug when concatenating records.
record.features = [
f for f in record.features if f.location is not None
and f.location.start <= f.location.end
]
for r in records:
if data.backbone_first and r.id == data.backbone_name:
r.is_backbone = True
repository.add_records(records, collection="parts")
# CREATE A CONNECTORS COLLECTION IF CONNECTORS ARE PROVIDED
connectors_collection = None
if len(data.connectors):
connector_records = records_from_data_files(data.connectors)
for r in records + connector_records:
set_record_topology(r, topology=data.topology)
r.seq = r.seq.upper()
repository.add_records(connector_records, collection="connectors")
connectors_collection = "connectors"
# SIMULATE!
self.logger(message="Simulating the assembly...")
if not data.use_assembly_plan:
# SCENARIO: SINGLE ASSEMBLY
parts = [r.id for r in records]
assembly = dc.Type2sRestrictionAssembly(
name="simulated_assembly",
parts=parts,
enzyme=data.enzyme,
expected_constructs="any_number",
connectors_collection=connectors_collection,
)
simulation = assembly.simulate(sequence_repository=repository)
n = len(simulation.construct_records)
self.logger(
message="Done (%d constructs found), writing report..." % n)
report_zip_data = simulation.write_report(
target="@memory", report_writer=report_writer)
return {
"file": {
"data": data_to_html_data(report_zip_data, "zip"),
"name": "assembly_simulation.zip",
"mimetype": "application/zip",
},
"errors": [str(e) for e in simulation.errors],
"n_constructs": len(simulation.construct_records),
"success": True,
}
else:
# SCENARIO: FULL ASSEMBLY PLAN
filelike = file_to_filelike_object(data.assembly_plan)
assembly_plan = dc.AssemblyPlan.from_spreadsheet(
assembly_class=dc.Type2sRestrictionAssembly,
path=filelike,
connectors_collection=connectors_collection,
expect_no_unused_parts=data.no_skipped_parts,
expected_constructs=1
if data.single_assemblies else "any_number",
name="_".join(data.assembly_plan.name.split(".")[:-1]),
is_csv=data.assembly_plan.name.lower().endswith(".csv"),
logger=self.logger,
)
simulation = assembly_plan.simulate(sequence_repository=repository)
stats = simulation.compute_stats()
n_errors = stats["errored_assemblies"]
self.logger(message="Done (%d errors), writing report..." %
n_errors)
report_zip_data = simulation.write_report(
target="@memory",
assembly_report_writer=report_writer,
logger=self.logger,
)
errors = [
error
for assembly_simulation in simulation.assembly_simulations
for error in assembly_simulation.errors
]
return {
"file": {
"data": data_to_html_data(report_zip_data, "zip"),
"name": "%s.zip" % assembly_plan.name,
"mimetype": "application/zip",
},
"assembly_stats": stats,
"errors": [str(e) for e in errors],
"success": True,
}
self.logger(message="Simulating the assembly...")
import dnacauldron as dc
repository = dc.SequenceRepository()
repository.import_records(
collection="parts",
folder="genetic_parts",
use_file_names_as_ids=True,
topology="circular",
)
repository.import_records(
collection="emma_connectors",
folder="emma_connectors",
use_file_names_as_ids=True,
)
all_parts = list(repository.collections["parts"]) # part names, no connectors
assembly = dc.Type2sRestrictionAssembly(
name="assembly_with_connectors",
parts=all_parts,
connectors_collection="emma_connectors",
)
report_writer = dc.AssemblyReportWriter(include_mix_graphs=True)
simulation = assembly.simulate(sequence_repository=repository)
simulation.write_report("output", report_writer=report_writer)
print("Done! see output/ folder for the results.")
import dnacauldron as dc
import os
repository = dc.SequenceRepository()
repository.import_records(folder="parts", use_file_names_as_ids=True)
parts_list = list(repository.collections["parts"])
assembly = dc.Type2sRestrictionAssembly(
name="combinatorial_asm",
parts=parts_list,
expected_constructs="any_number",
)
simulation = assembly.simulate(sequence_repository=repository)
report_writer = dc.AssemblyReportWriter(include_mix_graphs=True,
include_part_plots=True)
simulation.write_report(
target=os.path.join("output", "combinatorial"),
report_writer=report_writer,
)
print("Done! see output/combinatorial folder for the results.")
def test_single_assembly_with_wrong_enzyme(tmpdir):
assembly = dc.Type2sRestrictionAssembly(parts=["partA", "partB", "partC"],
enzyme="BsaI")
simulation = assembly.simulate(sequence_repository=repo)
assert simulation.construct_records == []