def promoter_assemblies_build_more_than_384():
utr_linkers = [
"UTR1-RBS1",
"UTR1-RBS2",
"UTR1-RBS3",
"UTR2-RBS1",
"UTR2-RBS2",
"UTR2-RBS3",
"UTR3-RBS1",
"UTR3-RBS2",
"UTR3-RBS3",
]
promoter_assemblies = []
for utr_linker in utr_linkers:
promoter_assemblies += [
bsb.BasicAssembly(
f"promoter_construct_{ind}_{utr_linker}",
bsb.BASIC_SEVA_PARTS["v0.1"]["26"],
bsb.BASIC_BIOLEGIO_LINKERS["v0.1"]["LMP"],
promoter,
bsb.BASIC_BIOLEGIO_LINKERS["v0.1"][utr_linker],
bsb.BASIC_CDS_PARTS["v0.1"]["sfGFP"],
bsb.BASIC_BIOLEGIO_LINKERS["v0.1"]["LMS"],
) for ind, promoter in enumerate(
bsb.BASIC_PROMOTER_PARTS["v0.1"].values())
]
return bsb.BasicBuild(*promoter_assemblies)
def small_build_example():
return bsb.BasicBuild(
bsb.BasicAssembly(
"First_Assembly_With_18",
bsb.BASIC_SEVA_PARTS["v0.1"]["18"],
bsb.BASIC_BIOLEGIO_LINKERS["v0.1"]["LMP"],
bsb.BASIC_CDS_PARTS["v0.1"]["sfGFP"],
bsb.BASIC_BIOLEGIO_LINKERS["v0.1"]["LMS"],
),
bsb.BasicAssembly(
"Second_Assembly_With_26",
bsb.BASIC_SEVA_PARTS["v0.1"]["26"],
bsb.BASIC_BIOLEGIO_LINKERS["v0.1"]["LMP"],
bsb.BASIC_CDS_PARTS["v0.1"]["sfGFP"],
bsb.BASIC_BIOLEGIO_LINKERS["v0.1"]["LMS"],
),
)
def five_part_assembly(five_part_assembly_parts, five_part_assembly_linkers):
zipped_parts_linkers = zip(five_part_assembly_linkers,
five_part_assembly_parts)
parts_linkers = []
for part_linker in zipped_parts_linkers:
parts_linkers += list(part_linker)
print([part_linker.id for part_linker in parts_linkers])
print([type(part_linker) for part_linker in parts_linkers])
return bsb.BasicAssembly("5_part", *parts_linkers)
def test_assembly_exception_same_utr_linker(cmr_p15a_basicpart, gfp_basicpart):
from basicsynbio.main import AssemblyException
with pytest.raises(
AssemblyException, match="BasicAssembly initiated with UTR1-S used 2 times."
):
bsb.BasicAssembly(
"test",
cmr_p15a_basicpart,
bsb.BASIC_BIOLEGIO_LINKERS["v0.1"]["UTR1-RBS1"],
gfp_basicpart,
bsb.BASIC_BIOLEGIO_LINKERS["v0.1"]["UTR1-RBS2"],
)
def build_json():
promoter_assemblies = (bsb.BasicAssembly(
f"promoter_construct_{ind}",
bsb.BASIC_SEVA_PARTS["v0.1"]["26"],
bsb.BASIC_BIOLEGIO_LINKERS["v0.1"]["LMP"],
promoter,
bsb.BASIC_BIOLEGIO_LINKERS["v0.1"]["UTR1-RBS2"],
bsb.BASIC_CDS_PARTS["v0.1"]["sfGFP"],
bsb.BASIC_BIOLEGIO_LINKERS["v0.1"]["LMS"],
) for ind, promoter in enumerate(bsb.BASIC_PROMOTER_PARTS["v0.1"].values())
)
build = bsb.BasicBuild(*promoter_assemblies)
return build
def test_assembly_error(gfp_basicpart, cmr_p15a_basicpart):
import basicsynbio.main as bsb_main
with pytest.raises(bsb_main.AssemblyException):
bsb.BasicAssembly("test", gfp_basicpart, cmr_p15a_basicpart)