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feat: Add strand to FusionVariant output #157

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Merged
susannasiebert merged 11 commits into from
Mar 28, 2025
Merged

feat: Add strand to FusionVariant output #157

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ea9297b
Store changes to add strand
jarbesfeld Mar 23, 2025
a80ffd2
Remove strand from CoordinateQuery
jarbesfeld Mar 24, 2025
d350aa7
Update fusion output structure
jarbesfeld Mar 24, 2025
0996df8
Implement ExonCoordinate class and ensure that coordinates get correc…
susannasiebert Mar 24, 2025
771e370
Add updated tests for BCR::AB1 fusion
jarbesfeld Mar 24, 2025
6c1db21
Update tests
susannasiebert Mar 24, 2025
02541e4
Update tests for exon and exon offset
jarbesfeld Mar 25, 2025
fe0d0b1
Add tests for attributes and fix naming in graphql payload
jarbesfeld Mar 25, 2025
33c92f4
Allow nullable complex fields
susannasiebert Mar 25, 2025
190139c
Set exon_offset to 0 instead of Null
susannasiebert Mar 25, 2025
df5c180
Update tests
susannasiebert Mar 25, 2025
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Implement ExonCoordinate class and ensure that coordinates get correc… 
…tly parsed to (Exon)Coordinate objects
  • Loading branch information
@susannasiebert
susannasiebert committed Mar 24, 2025
commit 0996df8e5a8fd854f2e3e7dbe021e024c17c4f97
59 changes: 45 additions & 14 deletions civicpy/civic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,8 +41,12 @@

CIVIC_TO_PYCLASS = {
'evidence_items': 'evidence',
'five_prime_coordinates': 'coordinates',
'three_prime_ccodinates': 'coordinates',
'five_prime_coordinates': 'coordinate',
'three_prime_coordinates': 'coordinate',
'five_prime_start_exon_coordinates': 'exon_coordinate',
'five_prime_end_exon_coordinates': 'exon_coordinate',
'three_prime_start_exon_coordinates': 'exon_coordinate',
'three_prime_end_exon_coordinates': 'exon_coordinate',
}


Expand Down Expand Up @@ -438,7 +442,7 @@ def __init__(self, partial=False, **kwargs):
else:
raise AttributeError('Expected {} attribute for {}, none found.'.format(field, self.type))
is_compound = isinstance(v, list)
cls = get_class(field)
cls = get_class(CIVIC_TO_PYCLASS.get(field, field))
if is_compound:
result = list()
for data in v:
Expand Down Expand Up @@ -977,10 +981,12 @@ class FusionVariant(Variant):
'vicc_compliant_name',
})
_COMPLEX_FIELDS = Variant._COMPLEX_FIELDS.union({
'five_prime_exon_start_coordinates',
'five_prime_exon_end_coordinates',
'three_prime_exon_start_coordinates',
'three_prime_exon_end_coordinates',
'five_prime_coordinates',
'three_prime_coordinates',
'five_prime_start_exon_coordinates',
'five_prime_end_exon_coordinates',
'three_prime_start_exon_coordinates',
'three_prime_end_exon_coordinates',
})

@property
Expand Down Expand Up @@ -1728,7 +1734,7 @@ def update(self):
return NotImplementedError


class Coordinates(CivicAttribute):
class Coordinate(CivicAttribute):
_SIMPLE_FIELDS = CivicAttribute._SIMPLE_FIELDS.union({
'chromosome',
'start',
Expand All @@ -1740,11 +1746,32 @@ class Coordinates(CivicAttribute):
'reference_build',
})

def __repr__(self):
return '<CIViC Coordinate>'.format(self.type)

def __init__(self, **kwargs):
super().__init__(**kwargs)


class ExonCoordinate(CivicAttribute):
_SIMPLE_FIELDS = CivicAttribute._SIMPLE_FIELDS.union({
'chromosome',
'ensembl_id',
'ensembl_version',
'exon',
'exon_offset',
'exon_offset_direction',
'reference_build',
'representative_transcript',
'start',
'stop',
'strand',
})

def __repr__(self):
return '<CIViC ExonCoordinate>'.format(self.type)

def __init__(self, **kwargs):
if self.reference_bases in ['', '-']:
self.reference_bases = None
if self.variant_bases in ['', '-']:
self.variant_bases = None
super().__init__(**kwargs)


Expand Down Expand Up @@ -1905,6 +1932,10 @@ def _postprocess_response_element(e, element):
elif build == 'GRCH38':
build = 'GRCh38'
e['coordinates']['reference_build'] = build
if e['coordinates']['reference_bases'] in ['', '-']:
e['coordinates']['reference_bases'] = None
if e['coordinates']['variant_bases'] in ['', '-']:
e['coordinates']['variant_bases'] = None
elif e['__typename'] == 'FactorVariant':
e['subtype'] = 'factor_variant'
elif e['__typename'] == 'FusionVariant':
Expand Down Expand Up @@ -2400,7 +2431,7 @@ def get_all_variants(include_status=['accepted', 'submitted', 'rejected'], allow
:param bool allow_cached: Indicates whether or not object retrieval from CACHE is allowed. If **False** it will query the CIViC database directly.
:returns: A list of :class:`Variant` objects.
"""
variants = _get_elements_by_ids('variant', allow_cached=allow_cached, get_all=True)
variants = _get_elements_by_ids('variant', allow_cached=allow_cached, get_all=allow_cached)
if include_status:
assert CACHE.get('evidence_items_all_ids', False)
assert CACHE.get('assertions_all_ids', False)
Expand All @@ -2422,7 +2453,7 @@ def get_all_gene_variants(include_status=['accepted', 'submitted', 'rejected'],
:param bool allow_cached: Indicates whether or not object retrieval from CACHE is allowed. If **False** it will query the CIViC database directly.
:returns: A list of :class:`Variant` objects of **subtype** **gene_variant**.
"""
variants = get_all_variants(include_status=include_status, allow_cached=True)
variants = get_all_variants(include_status=include_status, allow_cached=allow_cached)
return [v for v in variants if v.subtype == 'gene_variant']


Expand Down
127 changes: 119 additions & 8 deletions civicpy/graphql_payloads.py
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Original file line number Diff line number Diff line change
Expand Up @@ -230,6 +230,81 @@ def _construct_get_variant_payload():
variant_bases: variantBases
}
}
... on FusionVariant {
vicc_compliant_name: viccCompliantName
five_prime_coordinates: fivePrimeCoordinates {
reference_build: referenceBuild
ensembl_version: ensemblVersion
chromosome
representative_transcript: representativeTranscript
start
stop
reference_bases: referenceBases
variant_bases: variantBases
}
three_prime_coordinates: threePrimeCoordinates {
reference_build: referenceBuild
ensembl_version: ensemblVersion
chromosome
representative_transcript: representativeTranscript
start
stop
reference_bases: referenceBases
variant_bases: variantBases
}
five_prime_exon_start_coordinates: fivePrimeStartExonCoordinates {
chromosome
ensembl_id: ensemblId
ensembl_version: ensemblVersion
exon
exon_offset: exonOffset
exon_offset_direction: exonOffsetDirection
reference_build: referenceBuild
representative_transcript: representativeTranscript
start
stop
strand
}
five_prime_exon_end_coordinates: fivePrimeEndExonCoordinates {
chromosome
ensembl_id: ensemblId
ensembl_version: ensemblVersion
exon
exon_offset: exonOffset
exon_offset_direction: exonOffsetDirection
reference_build: referenceBuild
representative_transcript: representativeTranscript
start
stop
strand
}
three_prime_exon_start_coordinates: threePrimeStartExonCoordinates {
chromosome
ensembl_id: ensemblId
ensembl_version: ensemblVersion
exon
exon_offset: exonOffset
exon_offset_direction: exonOffsetDirection
reference_build: referenceBuild
representative_transcript: representativeTranscript
start
stop
strand
}
three_prime_exon_end_coordinates: threePrimeEndExonCoordinates {
chromosome
ensembl_id: ensemblId
ensembl_version: ensemblVersion
exon
exon_offset: exonOffset
exon_offset_direction: exonOffsetDirection
reference_build: referenceBuild
representative_transcript: representativeTranscript
start
stop
strand
}
}
... on FactorVariant {
ncit_id: ncitId
}
Expand Down Expand Up @@ -288,37 +363,73 @@ def _construct_get_all_variants_payload():
}
... on FusionVariant {
vicc_compliant_name: viccCompliantName
five_prime_exon_start_coordinates: fivePrimeStartExonCoordinates {
five_prime_coordinates: fivePrimeCoordinates {
reference_build: referenceBuild
ensembl_version: ensemblVersion
chromosome
representative_transcript: representativeTranscript
start
stop
strand
reference_bases: referenceBases
variant_bases: variantBases
}
five_prime_exon_end_coordinates: fivePrimeEndExonCoordinates {
three_prime_coordinates: threePrimeCoordinates {
reference_build: referenceBuild
ensembl_version: ensemblVersion
chromosome
representative_transcript: representativeTranscript
start
stop
strand
reference_bases: referenceBases
variant_bases: variantBases
}
three_prime_exon_start_coordinates: threePrimeStartExonCoordinates {
reference_build: referenceBuild
ensembl_version: ensemblVersion
five_prime_start_exon_coordinates: fivePrimeStartExonCoordinates {
chromosome
ensembl_id: ensemblId
ensembl_version: ensemblVersion
exon
exon_offset: exonOffset
exon_offset_direction: exonOffsetDirection
reference_build: referenceBuild
representative_transcript: representativeTranscript
start
stop
strand
}
three_prime_exon_end_coordinates: threePrimeEndExonCoordinates {
five_prime_end_exon_coordinates: fivePrimeEndExonCoordinates {
chromosome
ensembl_id: ensemblId
ensembl_version: ensemblVersion
exon
exon_offset: exonOffset
exon_offset_direction: exonOffsetDirection
reference_build: referenceBuild
representative_transcript: representativeTranscript
start
stop
strand
}
three_prime_start_exon_coordinates: threePrimeStartExonCoordinates {
chromosome
ensembl_id: ensemblId
ensembl_version: ensemblVersion
exon
exon_offset: exonOffset
exon_offset_direction: exonOffsetDirection
reference_build: referenceBuild
representative_transcript: representativeTranscript
start
stop
strand
}
three_prime_end_exon_coordinates: threePrimeEndExonCoordinates {
chromosome
ensembl_id: ensemblId
ensembl_version: ensemblVersion
exon
exon_offset: exonOffset
exon_offset_direction: exonOffsetDirection
reference_build: referenceBuild
representative_transcript: representativeTranscript
start
stop
Expand Down