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 main():
'''main method.'''
doc = Document()
doc.read('sbol.xml')
for seq in doc.sequences:
print seq.identity.get()
print seq.elements.get()
doc.write('out.xml')
def read(filename):
'''Parses SBOL v1.'''
doc = Document()
doc.read(filename)
comp_def = doc.componentDefinitions[0]
params = _read_dna_comp(comp_def)
params.update({'seq': doc.sequences[0].elements})
dna = DNA(**params)
for annot in comp_def.sequenceAnnotations:
_read_annot(dna, annot)
return dna
def to_query(filename, taxonomy_id):
'''Convert SBOL documents to PartsGenie query.'''
doc = Document()
doc.read(filename)
return _to_query(doc, taxonomy_id)
