Skip to content

conversion seqfeat_anno and tests #367

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Gonza10V wants to merge 5 commits into
base: develop
Choose a base branch
from
Open

conversion seqfeat_anno and tests #367

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
36c252b
conversion seqfeat_anno and tests
Gonza10V Oct 22, 2025
f325002
implementig feedback
Gonza10V Oct 23, 2025
b4856dc
saved changes
Gonza10V Oct 23, 2025
5f72424
changing identity by uri while creating seqanno
Gonza10V Oct 23, 2025
f920556
solving typos on test
Gonza10V Oct 23, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
98 changes: 79 additions & 19 deletions sbol_utilities/sbol3_sbol2_conversion.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -389,9 +389,37 @@ def visit_sequence(self, seq3: sbol3.Sequence):
# Map over all other TopLevel properties and extensions not covered by the constructor
self._convert_toplevel(seq3, seq2)

def visit_sequence_feature(self, a: sbol3.SequenceFeature):
# Priority: 1
raise NotImplementedError('Conversion of SequenceFeature from SBOL3 to SBOL2 not yet implemented')
def visit_sequence_feature(self, seqfeat3: sbol3.SequenceFeature):
# Priority: 1
# SBOL 2.x SequenceAnnotation objects map to SBOL 3.x SequenceFeature objects if they do not have a component.
# If they do have a component, their locations are added to the corresponding SBOL3 SubComponent.

# convert locations
locations2 = []
if seqfeat3.locations:
Copy link
Contributor

@jakebeal jakebeal Oct 23, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This can all be done with just a single list comprehension:
locations2 = [loc3.accept(self) for loc3 in seqfeat3.locations]

Copy link
Contributor Author

@Gonza10V Gonza10V Oct 23, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

implemented

Copy link
Contributor Author

@Gonza10V Gonza10V Oct 23, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I also realized that I dont need to convert name, description, wasDerivedFrom, nor wasGeneratedBy as those are handled by _convert_identified. So I'm removing those.

for loc3 in seqfeat3.locations:
if type(loc3) is sbol3.location.Range:
raise NotImplementedError('Conversion of Range from SBOL3 to SBOL2 not yet implemented')
elif type(loc3) is sbol3.location.Cut:
raise NotImplementedError('Conversion of Cut from SBOL3 to SBOL2 not yet implemented')
elif type(loc3) is sbol3.location.EntireSequence:
raise NotImplementedError('Conversion of EntireSequence from SBOL3 to SBOL2 not yet implemented')
else: raise ValueError(f'Unknown location type {type(loc3)}, SequenceFeature cannot convert to SBOL2')
else: raise ValueError('SequenceFeature must have at least one location')
Copy link
Contributor

@jakebeal jakebeal Oct 23, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

No need to check this if we've validated in advance.

Copy link
Contributor Author

@Gonza10V Gonza10V Oct 23, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

removed with the implementation of the list comprehension


# Create SBOL2 SequenceAnnotation
seqanno2 = sbol2.SequenceAnnotation(identity=self._sbol3_identity(seqfeat3),
locations = locations2,
roles = seqfeat3.roles,
name = seqfeat3.name,
description = seqfeat3.description,
wasDerivedFrom = seqfeat3.derived_from,
wasGeneratedBy = seqfeat3.generated_by,
version=self._sbol2_version(seqfeat3) )

self._convert_identified(seqfeat3, seqanno2)
return seqanno2, locations2


def visit_singular_unit(self, a: sbol3.SingularUnit):
# Priority: 4
Expand Down Expand Up @@ -752,7 +780,7 @@ def visit_range(self, r2: sbol2.Range):
cdef = r2.parent.parent
ns = self._sbol3_namespace(cdef)
seq_stub = sbol3.Sequence(f'{ns}/{cdef.displayId}Seq/', namespace=ns)
cdef.sequence = seq_stup
cdef.sequence = seq_stub
cdef.doc.add(seq_stub)
r3 = sbol3.Range(seq_ref, r2.start, r2.end)
self._convert_identified(r2, r3)
Expand All @@ -772,21 +800,53 @@ def visit_sequence(self, seq2: sbol2.Sequence):
# Map over all other TopLevel properties and extensions not covered by the constructor
self._convert_toplevel(seq2, seq3)

def visit_sequence_annotation(self, sa2: sbol2.SequenceAnnotation):
# component URIRef 0..1
# orientation URI 0..1
locations = []
for l2 in sa2.locations:
if type(l2) == sbol2.Range:
l3 = self.visit_range(l2)
else:
raise NotImplementedError('Conversion of {type(l2)} from SBOL2 to SBOL3 not yet implemented')
locations.append(l3)

f3 = sbol3.SequenceFeature(locations)
f3.roles = sa2.roles
self._convert_identified(sa2, f3)
return f3, locations
def visit_sequence_annotation(self, seqanno2: sbol2.SequenceAnnotation):
# Priority: 1
# SBOL 2.x SequenceAnnotation objects map to SBOL 3.x SequenceFeature objects if they do not have a component.
# If they do have a component, their locations are added to the corresponding SBOL3 SubComponent.

# convert locations
locations3 = []
Copy link
Contributor

@jakebeal jakebeal Oct 23, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Similar notes to above for converting to a list comprehension and dealing with exception handling. For pySBOL2 there's no accept function to call, but you can move the if/elif into a nested function and call that from the list comprehension.

if seqanno2.locations:
for loc2 in seqanno2.locations:
if type(loc2) is sbol2.location.Range:
l3 = self.visit_range(loc2)
elif type(loc2) is sbol2.location.Cut:
raise NotImplementedError('Conversion of Cut from SBOL2 to SBOL3 not yet implemented')
elif type(loc2) is sbol2.location.GenericLocation:
raise NotImplementedError('Conversion of GenericLocation from SBOL2 to SBOL3 not yet implemented')
else: raise ValueError(f'Unknown location type {type(loc2)}, SequenceAnnotation cannot convert to SBOL3')
locations3.append(l3)
else:
raise ValueError('SequenceAnnotation must have at least one location')

# Create SBOL3 SequenceFeature
if seqanno2.component:
feature3 = sbol3.SubComponent(namespace=self._sbol3_namespace(seqanno2),
Copy link
Contributor

@jakebeal jakebeal Oct 23, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

These aren't top-levels, so they don't take a namespace - they're going to get their name from their parent.

Copy link
Contributor Author

@Gonza10V Gonza10V Oct 23, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

removed

instance_of=seqanno2.component, #
locations=locations3,
roles=seqanno2.roles,
name=seqanno2.name,
description=seqanno2.description,
derived_from=seqanno2.wasDerivedFrom,
generated_by=seqanno2.wasGeneratedBy
)

else:
feature3 = sbol3.SequenceFeature(namespace=self._sbol3_namespace(seqanno2),
identity=self._sbol3_identity(seqanno2),
locations=locations3,
roles=seqanno2.roles,
name=seqanno2.name,
description=seqanno2.description,
derived_from=seqanno2.wasDerivedFrom,
generated_by=seqanno2.wasGeneratedBy
)


self._convert_identified(seqanno2, feature3)
return feature3, locations3


def visit_sequence_constraint(self, seq2: sbol2.sequenceconstraint.SequenceConstraint):
# Priority: 2
Expand Down
33 changes: 33 additions & 0 deletions test/test_files/sbol_3to2_sequence_annotation.nt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
<rdf:RDF xmlns:brick="https://brickschema.org/schema/Brick#" xmlns:csvw="http://www.w3.org/ns/csvw#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:dcmitype="http://purl.org/dc/dcmitype/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dcam="http://purl.org/dc/dcam/" xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:geo="http://www.opengis.net/ont/geosparql#" xmlns:odrl="http://www.w3.org/ns/odrl/2/" xmlns:org="http://www.w3.org/ns/org#" xmlns:prof="http://www.w3.org/ns/dx/prof/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:qb="http://purl.org/linked-data/cube#" xmlns:schema="https://schema.org/" xmlns:sh="http://www.w3.org/ns/shacl#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:sosa="http://www.w3.org/ns/sosa/" xmlns:ssn="http://www.w3.org/ns/ssn/" xmlns:time="http://www.w3.org/2006/time#" xmlns:vann="http://purl.org/vocab/vann/" xmlns:void="http://rdfs.org/ns/void#" xmlns:wgs="https://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:backport="http://sboltools.org/backport#" xmlns:sbol="http://sbols.org/v2#">
<sbol:Sequence rdf:about="https://github.com/sequence1">
<sbol:persistentIdentity rdf:resource="https://github.com/sequence1"/>
<sbol:elements>gattaca</sbol:elements>
<sbol:displayId>sequence1</sbol:displayId>
<backport:sbol3namespace rdf:resource="https://github.com/"/>
<sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
</sbol:Sequence>
<sbol:ComponentDefinition rdf:about="https://github.com/component1">
<sbol:displayId>component1</sbol:displayId>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="https://github.com/component1/SequenceFeature1">
<sbol:location>
<sbol:Range rdf:about="https://github.com/component1/SequenceFeature1/Range1">
<sbol:displayId>Range1</sbol:displayId>
<sbol:persistentIdentity rdf:resource="https://github.com/component1/SequenceFeature1/Range1"/>
<sbol:end>3</sbol:end>
<sbol:start>1</sbol:start>
</sbol:Range>
</sbol:location>
<sbol:displayId>SequenceFeature1</sbol:displayId>
<dcterms:title>promoter_feature</dcterms:title>
<sbol:role rdf:resource="https://identifiers.org/SO:0000167"/>
<sbol:persistentIdentity rdf:resource="https://github.com/component1/SequenceFeature1"/>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<backport:sbol3identity rdf:resource="https://github.com/component1"/>
<sbol:persistentIdentity rdf:resource="https://github.com/component1"/>
<backport:sbol3namespace rdf:resource="https://github.com/"/>
<sbol:sequence rdf:resource="https://github.com/sequence1"/>
</sbol:ComponentDefinition>
</rdf:RDF>
35 changes: 35 additions & 0 deletions test/test_files/sbol_3to2_sequence_feature.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:sbol="http://sbols.org/v3#"
>
<rdf:Description rdf:about="https://github.com/component1">
<sbol:displayId>component1</sbol:displayId>
<rdf:type rdf:resource="http://sbols.org/v3#Component"/>
<sbol:hasNamespace rdf:resource="https://github.com/"/>
<sbol:type rdf:resource="https://identifiers.org/SBO:0000251"/>
<sbol:hasSequence rdf:resource="https://github.com/sequence1"/>
<sbol:hasFeature rdf:resource="https://github.com/component1/SequenceFeature1"/>
</rdf:Description>
<rdf:Description rdf:about="https://github.com/sequence1">
<sbol:displayId>sequence1</sbol:displayId>
<rdf:type rdf:resource="http://sbols.org/v3#Sequence"/>
<sbol:hasNamespace rdf:resource="https://github.com/"/>
<sbol:elements>gattaca</sbol:elements>
<sbol:encoding rdf:resource="https://identifiers.org/edam:format_1207"/>
</rdf:Description>
<rdf:Description rdf:about="https://github.com/component1/SequenceFeature1/Range1">
<sbol:displayId>Range1</sbol:displayId>
<rdf:type rdf:resource="http://sbols.org/v3#Range"/>
<sbol:hasSequence rdf:resource="https://github.com/sequence1"/>
<sbol:start rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">1</sbol:start>
<sbol:end rdf:datatype="http://www.w3.org/2001/XMLSchema#integer">3</sbol:end>
</rdf:Description>
<rdf:Description rdf:about="https://github.com/component1/SequenceFeature1">
<sbol:displayId>SequenceFeature1</sbol:displayId>
<sbol:name>promoter_feature</sbol:name>
<rdf:type rdf:resource="http://sbols.org/v3#SequenceFeature"/>
<sbol:role rdf:resource="https://identifiers.org/SO:0000167"/>
<sbol:hasLocation rdf:resource="https://github.com/component1/SequenceFeature1/Range1"/>
</rdf:Description>
</rdf:RDF>
7 changes: 6 additions & 1 deletion test/test_sbol2_sbol3_direct.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -309,6 +309,9 @@ def test_functionalcomponent_conversion(self):
def test_interaction_conversion(self):
self.handle_2to3_conversion('sbol_3to2_interaction.xml', 'sbol_3to2_interaction.nt')

def test_seq_annotation_conversion(self):
self.handle_2to3_conversion('sbol_3to2_sequence_annotation.nt', 'sbol_3to2_sequence_feature.nt')


class TestDirectSBOL3SBOL2Conversion(unittest.TestCase):

Expand Down Expand Up @@ -373,6 +376,8 @@ def test_identity_conversion(self):
def test_interaction_conversion(self):
self.handle_3to2_conversion('sbol_3to2_interaction.nt', 'sbol_3to2_interaction.xml')


def test_seq_feature_conversion(self):
self.handle_3to2_conversion('sbol_3to2_sequence_feature.nt', 'sbol_3to2_sequence_annotation.xml')

if __name__ == '__main__':
unittest.main()
Loading