def example1():
'''Simple example.'''
setHomespace("http://sys-bio.org")
doc = Document()
gene = ComponentDefinition("BB0001")
promoter = ComponentDefinition("R0010")
cds = ComponentDefinition("B0032")
rbs = ComponentDefinition("E0040")
terminator = ComponentDefinition("B0012")
promoter.roles.set(SO_PROMOTER)
cds.roles.set(SO_CDS)
rbs.roles.set(SO_RBS)
terminator.roles.set(SO_TERMINATOR)
doc.addComponentDefinition(gene)
doc.addComponentDefinition(promoter)
doc.addComponentDefinition(cds)
doc.addComponentDefinition(rbs)
doc.addComponentDefinition(terminator)
gene.assemble([promoter, rbs, cds, terminator])
first = gene.getFirstComponent()
print first.identity.get()
last = gene.getLastComponent()
print last.identity.get()
# promoter_seq = Sequence("R0010", "ggctgca")
# rbs_seq = Sequence("B0032", "aattatataaa")
# cds_seq = Sequence("E0040", "atgtaa")
# terminator_seq = Sequence("B0012", "attcga")
# gene_seq = Sequence("BB0001")
# doc.addSequence(promoter_seq)
# doc.addSequence(cds_seq)
# doc.addSequence(rbs_seq)
# doc.addSequence(terminator_seq)
# doc.addSequence(gene_seq)
# promoter.sequence.set(promoter_seq.identity.get())
# cds.sequence.set(cds_seq.identity.get())
# rbs.sequence.set(rbs_seq.identity.get())
# terminator.sequence.set(terminator_seq.identity.get())
# gene.sequence.set(gene_seq.identity.get())
# gene_seq.assemble()
# print gene_seq.elements.get()
doc.write("gene_cassette.xml")
# Round trip...
doc.write('gene_cassette.xml')
new_doc = Document()
new_doc.read('gene_cassette.xml')
new_doc.write('gene_cassette_out.xml')
def test1():
sbol.setHomespace('http://sbol_prefix.org')
doc = sbol.Document()
pTetR = sbol.ComponentDefinition("test_promoter_1", sbol.BIOPAX_DNA)
pTetR.roles = sbol.SO_PROMOTER
doc.addComponentDefinition(pTetR)
results = doc.write("pysbol_output.xml")
return results
def _UploadDoc(doc, registry='https://synbiohub.org'):
""" A tabular csv file containing columns: Name, Type, Part is read
and each part in added to the SBOL doc.
Part type should is overriden by the ontology definition in the registry """
namespace = "http://synbiochem.co.uk"
sbol.setHomespace(namespace)
repo = sbol.PartShop(registry)
repo.login(os.getenv('IBISBA_SYNBIOHUB_USERNAME'),
os.getenv('IBISBA_SYNBIOHUB_PASSWORD'))
doc.displayId = 'E_coli_Parts'
doc.name = 'A collection of genetic parts for engineering E. coli'
doc.description = 'Standard regulatory genetic parts for building E. coli combinatorial libraries in the Galaxy-SynbioCAD. The collection contains a selection of commonly-used origins of replication, resistance cassettes, and inducible promoters.'
repo.submit(doc)
def crispr_test():
'''Simple example.'''
setHomespace('http://sys-bio.org')
doc = Document()
mkate, _ = _add_comp_def(doc, 'mKate')
gal4vp16, _ = _add_comp_def(doc, 'gal4vp16')
pconst, _ = _add_comp_def(doc, 'pconst', SO_PROMOTER, 'atgtaa')
mkate_cds, _ = _add_comp_def(doc, 'mkate_cds', SO_CDS, 'attcga')
gal4vp16_cds, _ = _add_comp_def(doc, 'gal4vp16_cds', SO_CDS, 'attcga')
mkate_gene, mkate_gene_seq = _add_comp_def(doc, 'mkate_gene')
gal4vp16_gene, gal4vp16_gene_seq = _add_comp_def(doc, 'gal4vp16_gene')
mkate_gene.assemble([pconst, mkate_cds])
gal4vp16_gene.assemble([pconst, gal4vp16_cds])
mkate_gene_seq.assemble()
print mkate_gene_seq.elements.get()
gal4vp16_gene_seq.assemble()
print gal4vp16_gene_seq.elements.get()
doc.write('crispr.xml')
def _convert(rct_uniprot, tirs, max_prot_per_react):
'''Convert.'''
setHomespace('http://liverpool.ac.uk')
doc = Document()
for rct, uniprot_ids_set in rct_uniprot.items():
# Specify uniprot-specific assembly region placeholders:
# (Provides consistent assembly sequence for each reaction group.)
_5p_assembly = ComponentDefinition('%s_5_prime_assembly' % rct)
_5p_assembly.roles = dna_utils.SO_ASS_COMP
_3p_assembly = ComponentDefinition('%s_3_prime_assembly' % rct)
_3p_assembly.roles = dna_utils.SO_ASS_COMP
doc.addComponentDefinition([_5p_assembly, _3p_assembly])
for uniprot_id in uniprot_ids_set[:max_prot_per_react]:
if tirs:
for tir in tirs:
_add_gene(doc, uniprot_id, tir, _5p_assembly, _3p_assembly)
else:
_add_gene(doc, uniprot_id, None, _5p_assembly, _3p_assembly)
return doc
def crispr_tutorial_short():
sbol.setHomespace('http://sbols.org/CRISPR_Example')
doc = sbol.Document()
target_gene = sbol.ComponentDefinition("target_gene", sbol.BIOPAX_DNA)
target_gene.roles = sbol.SO_PROMOTER
doc.addComponentDefinition(target_gene)
target = sbol.ComponentDefinition("target", sbol.BIOPAX_PROTEIN)
doc.addComponentDefinition(target)
CRISPR_Template = sbol.ModuleDefinition("CRISPR_Template")
doc.addModuleDefinition(CRISPR_Template)
target_gene_fc = CRISPR_Template.functionalComponents.create("target_gene_fc")
target_gene_fc.definition = target_gene.identity
target_gene_fc.access = sbol.SBOL_ACCESS_PUBLIC
target_gene_fc.direction = sbol.SBOL_DIRECTION_IN_OUT
target_fc = CRISPR_Template.functionalComponents.create("target_fc")
target_fc.definition = target.identity
target_fc.access = sbol.SBOL_ACCESS_PUBLIC
target_fc.direction = sbol.SBOL_DIRECTION_IN_OUT
target_generic_gene_inhibition = CRISPR_Template.interactions.create("target_gene_inhibition_interaction")
target_generic_gene_inhibition.types = sbol.SBO_GENETIC_PRODUCTION
target_gene_participation = target_generic_gene_inhibition.participations.create("target_gene_participation")
target_gene_participation.roles = sbol.SBO_PROMOTER
target_gene_participation.participant = target_gene_fc.identity
target_participation = target_generic_gene_inhibition.participations.create("target_participation")
target_participation.roles = sbol.SBO_PRODUCT
target_participation.participant = target_fc.identity
gRNA_gene = sbol.ComponentDefinition("gRNA_gene",sbol.BIOPAX_DNA)
gRNA_gene.roles = sbol.SO_PROMOTER
doc.addComponentDefinition(gRNA_gene)
gRNA_b = sbol.ComponentDefinition("gRNA_b",sbol.BIOPAX_RNA)
gRNA_b.roles = sbol.SO_SGRNA
doc.addComponentDefinition(gRNA_b)
CRPb_circuit = sbol.ModuleDefinition("CRPb_characterization_Circuit")
doc.addModuleDefinition(CRPb_circuit)
gRNA_b_fc = CRPb_circuit.functionalComponents.create("gRNA_b_fc")
gRNA_b_fc.definition = gRNA_b.identity
gRNA_b_fc.access = sbol.SBOL_ACCESS_PUBLIC
gRNA_b_fc.direction = sbol.SBOL_DIRECTION_NONE
gRNA_b_fc.version = 1
gRNA_gene_fc = CRPb_circuit.functionalComponents.create("gRNA_gene_fc")
gRNA_gene_fc.definition = gRNA_gene.identity
gRNA_gene_fc.access = sbol.SBOL_ACCESS_PUBLIC
gRNA_gene_fc.direction = sbol.SBOL_DIRECTION_NONE
gRNA_gene_fc.version = 1
gRNA_b_production = CRPb_circuit.interactions.create("gRNA_b_production")
gRNA_b_production.types = sbol.SBO_GENETIC_PRODUCTION
gRNA_b_gene_participant = gRNA_b_production.participations.create("gRNA_b_gene")
gRNA_b_gene_participant.roles = sbol.SBO_PROMOTER
gRNA_b_gene_participant.participant = gRNA_gene_fc.identity
gRNA_b_participant = gRNA_b_production.participations.create("gRNA_b")
gRNA_b_participant.roles = sbol.SBO_PRODUCT
gRNA_b_participant.participant = gRNA_b_fc.identity
gRNA_b_BFP_deg = CRPb_circuit.interactions.create("gRNA_b_BFP_deg")
gRNA_b_BFP_deg.types = sbol.SBO_DEGRADATION
gRNA_b_BFP_participant = gRNA_b_BFP_deg.participations.create("gRNA_b_BFP")
gRNA_b_BFP_participant.roles = sbol.SBO_REACTANT
gRNA_b_BFP_participant.participant = gRNA_b_fc.identity
Template_Module = CRPb_circuit.modules.create("CRISPR_Template")
Template_Module.definition = CRISPR_Template.identity
gRNA_b_map = Template_Module.mapsTos.create("gRNA_b_map")
gRNA_b_map.refinement = sbol.SBOL_REFINEMENT_USE_LOCAL
gRNA_b_map.local = gRNA_b_fc.identity
gRNA_b_map.remote = gRNA_gene_fc.identity
gRNA_b_map.name = "Hnelo"
results = doc.write("CRISPR_example_short_2.xml")
print(results)
def __init__(self, *, namespace: str, trace: ProvenanceTrace = None):
# TODO: is it sufficient for homespace to be set at document init?
setHomespace(namespace)
self.doc = Document()
super().__init__(trace)