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 write(dna, filename=None):
'''Writes a Dna object to SBOL v2.'''
doc = Document()
comp_def = ComponentDefinition(dna['disp_id'])
doc.addComponentDefinition(comp_def)
_write_dna_comp(comp_def, dna)
seq = Sequence(get_disp_id(), dna['seq'], SBOL_ENCODING_IUPAC)
doc.addSequence(seq)
for feature in dna['features']:
annot = SequenceAnnotation(feature['disp_id'])
comp_def.sequenceAnnotations.add(annot)
_write_dna_comp(annot, feature)
rnge = Range(get_disp_id())
annot.locations.add(rnge)
rnge.start = feature['start']
rnge.end = feature['end']
rnge.orientation = SBOL_ORIENTATION_INLINE if feature['forward'] \
else SBOL_ORIENTATION_REVERSE_COMPLEMENT
doc.write(filename)
return doc
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 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 combinatorial1():
'''Combinatorial example.'''
libsbol.setHomespace('http://www.synbiochem.ac.uk')
doc = Document()
# SPECIFY POSITIONS #
# Specify top-level ComponentDefinition and positional Components....
top = ComponentDefinition('top')
pos1cd = ComponentDefinition('pos1cd')
pos2cd = ComponentDefinition('pos2cd')
pos3cd = ComponentDefinition('pos3cd')
doc.addComponentDefinition(top)
doc.addComponentDefinition(pos1cd)
doc.addComponentDefinition(pos2cd)
doc.addComponentDefinition(pos3cd)
pos1c = top.components.create('pos1c')
pos2c = top.components.create('pos2c')
pos3c = top.components.create('pos3c')
pos1c.definition.set(pos1cd.identity.get())
pos2c.definition.set(pos2cd.identity.get())
pos3c.definition.set(pos3cd.identity.get())
# Specify positional SequenceConstraints...
# pos1 - pos2 - pos3
pos_sq1 = top.sequenceConstraints.create('pos_sq1')
pos_sq1.subject.set(pos1c.identity.get())
pos_sq1.object.set(pos2c.identity.get())
pos_sq1.restriction.set(SBOL_RESTRICTION_PRECEDES)
pos_sq2 = top.sequenceConstraints.create('pos_sq2')
pos_sq2.subject.set(pos2c.identity.get())
pos_sq2.object.set(pos3c.identity.get())
pos_sq2.restriction.set(SBOL_RESTRICTION_PRECEDES)
# SPECIFY 'PARTS' #
# Specify ComponentDefinitions....
rbs1cd = ComponentDefinition('rbs1cd')
rbs2cd = ComponentDefinition('rbs2cd')
cds1cd = ComponentDefinition('cds1cd')
cds2cd = ComponentDefinition('cds2cd')
doc.addComponentDefinition(rbs1cd)
doc.addComponentDefinition(rbs2cd)
doc.addComponentDefinition(cds1cd)
doc.addComponentDefinition(cds2cd)
# Specify sequences...
rbs1_seq = Sequence('rbs1cd', 'aaaa', SBOL_ENCODING_IUPAC)
rbs2_seq = Sequence('rbs2cd', 'cccc', SBOL_ENCODING_IUPAC)
cds1_seq = Sequence('cds1cd', 'gggg', SBOL_ENCODING_IUPAC)
cds2_seq = Sequence('cds2cd', 'attcga', SBOL_ENCODING_IUPAC)
doc.addSequence(rbs1_seq)
doc.addSequence(rbs2_seq)
doc.addSequence(cds1_seq)
doc.addSequence(cds2_seq)
# Associate sequences with ComponentDefinition...
rbs1cd.sequence.set(rbs1_seq.identity.get())
rbs2cd.sequence.set(rbs2_seq.identity.get())
cds1cd.sequence.set(cds1_seq.identity.get())
cds2cd.sequence.set(cds2_seq.identity.get())
# In SBOL Compliant mode, use create methods to add child objects, instead
# of constructors and add methods (open-world mode)
rbs1c = top.components.create('rbs1c')
rbs2c = top.components.create('rbs2c')
cds1c = top.components.create('cds1c')
cds2c = top.components.create('cds2c')
# # Add components...
# rbs1c = Component('rbs1c')
# rbs2c = Component('rbs2c')
# cds1c = Component('cds1c')
# cds2c = Component('cds2c')
# top.components.add(rbs1c)
# top.components.add(rbs2c)
# top.components.add(cds1c)
# top.components.add(cds2c)
# Associate Components to ComponentDefintions...
rbs1c.definition.set(pos1cd.identity.get())
rbs2c.definition.set(pos1cd.identity.get())
cds1c.definition.set(pos2cd.identity.get())
cds2c.definition.set(pos2cd.identity.get())
# The following was causing a segmentation fault!!! Note that rbs1c
# already belongs to top.components.
# A child object can't belong to two parent objects.
# Unfortunately, this is a tricky error to catch...
# rbs1cd.components.add(rbs1c)
# rbs2cd.components.add(rbs2c)
# cds1cd.components.add(cds1c)
# cds2cd.components.add(cds2c)
# SPECIFY COMBINATORIAL CONSTRAINTS #
# Position 1 can be either rbs1c or rbs2...
combin_pos1_1 = top.sequenceConstraints.create('combin_pos1_1')
combin_pos1_1.subject.set(pos1c.identity.get())
combin_pos1_1.object.set(rbs1c.identity.get())
combin_pos1_1.restriction.set('can_be')
combin_pos1_2 = top.sequenceConstraints.create('combin_pos1_2')
combin_pos1_2.subject.set(pos1c.identity.get())
combin_pos1_2.object.set(rbs2c.identity.get())
combin_pos1_2.restriction.set('can_be')
# combin_pos1_1 = SequenceConstraint(
# 'combin_pos1_1', 'pos1c', 'rbs1c', 'can_be')
# combin_pos1_2 = SequenceConstraint(
# 'combin_pos1_2', 'pos1c', 'rbs2c', 'can_be')
# top.sequenceConstraints.add(combin_pos1_1)
# top.sequenceConstraints.add(combin_pos1_2)
# Position 2 can be either cds1c or cds2c...
combin_pos2_1 = top.sequenceConstraints.create('combin_pos2_1')
combin_pos2_1.subject.set(pos2c.identity.get())
combin_pos2_1.object.set(cds1c.identity.get())
combin_pos2_1.restriction.set('can_be')
combin_pos2_2 = top.sequenceConstraints.create('combin_pos2_2')
combin_pos2_2.subject.set(pos2c.identity.get())
combin_pos2_2.object.set(cds2c.identity.get())
combin_pos2_2.restriction.set('can_be')
# combin_pos2_1 = SequenceConstraint(
# 'combin_pos2_1', 'pos2c', 'cds1c', 'can_be')
# combin_pos2_2 = SequenceConstraint(
# 'combin_pos2_2', 'pos2c', 'cds2c', 'can_be')
# top.sequenceConstraints.add(combin_pos2_1)
# top.sequenceConstraints.add(combin_pos2_2)
# Position 3 can be either cds1c or cds2c...
combin_pos3_1 = top.sequenceConstraints.create('combin_pos3_1')
combin_pos3_1.subject.set(pos3c.identity.get())
combin_pos3_1.object.set(cds1c.identity.get())
combin_pos3_1.restriction.set('can_be')
combin_pos3_2 = top.sequenceConstraints.create('combin_pos3_2')
combin_pos3_2.subject.set(pos3c.identity.get())
combin_pos3_2.object.set(cds2c.identity.get())
combin_pos3_2.restriction.set('can_be')
# combin_pos3_1 = SequenceConstraint(
# 'combin_pos3_1', 'pos3c', 'cds1c', 'can_be')
# combin_pos3_2 = SequenceConstraint(
# 'combin_pos3_2', 'pos3c', 'cds2c', 'can_be')
# top.sequenceConstraints.add(combin_pos3_1)
# top.sequenceConstraints.add(combin_pos3_2)
# But the Component at Position 2 cannot be the same as Position 3...
combin_pos_not_eq = top.sequenceConstraints.create('combin_pos_not_eq')
combin_pos_not_eq.subject.set(pos2c.identity.get())
combin_pos_not_eq.object.set(pos3c.identity.get())
combin_pos_not_eq.restriction.set('not_equal')
# combin_pos_not_eq = SequenceConstraint(
# 'combin_pos_not_eq', 'pos2c', 'pos2c', 'not_equal')
# top.sequenceConstraints.add(combin_pos_not_eq)
for comp_def in doc.componentDefinitions:
print comp_def.identity.get()
doc.write('combinatorial.xml')
def to_query(filename, taxonomy_id):
'''Convert SBOL documents to PartsGenie query.'''
doc = Document()
doc.read(filename)
return _to_query(doc, taxonomy_id)
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 __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)
