Ejemplo n.º 1
0
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
Ejemplo n.º 3
0
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)
Ejemplo n.º 4
0
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')
Ejemplo n.º 5
0
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
Ejemplo n.º 6
0
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)
Ejemplo n.º 7
0
 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)