fountain-life-service-clients 3.30.0__py3-none-any.whl → 3.31.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- fountain_life_service_clients/genomics_service.py +200 -0
- {fountain_life_service_clients-3.30.0.dist-info → fountain_life_service_clients-3.31.0.dist-info}/METADATA +1 -1
- {fountain_life_service_clients-3.30.0.dist-info → fountain_life_service_clients-3.31.0.dist-info}/RECORD +4 -3
- {fountain_life_service_clients-3.30.0.dist-info → fountain_life_service_clients-3.31.0.dist-info}/WHEEL +0 -0
|
@@ -0,0 +1,200 @@
|
|
|
1
|
+
# This file was generated automatically. Do not edit it directly.
|
|
2
|
+
from typing import (
|
|
3
|
+
List,
|
|
4
|
+
Literal,
|
|
5
|
+
NotRequired,
|
|
6
|
+
Optional,
|
|
7
|
+
TypedDict,
|
|
8
|
+
Union,
|
|
9
|
+
Unpack,
|
|
10
|
+
cast,
|
|
11
|
+
)
|
|
12
|
+
|
|
13
|
+
from fountain_life_service_clients._base_client import (
|
|
14
|
+
AlphaConfig,
|
|
15
|
+
AlphaResponse,
|
|
16
|
+
BaseClient,
|
|
17
|
+
)
|
|
18
|
+
|
|
19
|
+
SearchVariantsRequest = TypedDict(
|
|
20
|
+
"SearchVariantsRequest",
|
|
21
|
+
{
|
|
22
|
+
"variantSetIds": str,
|
|
23
|
+
"include": NotRequired[str],
|
|
24
|
+
"sequenceType": NotRequired[Union[Literal["somatic"], Literal["germline"]]],
|
|
25
|
+
"gene": NotRequired[Union[str, List[str]]],
|
|
26
|
+
"aminoAcidChange": NotRequired[Union[str, List[str]]],
|
|
27
|
+
"drugAssociations": NotRequired[bool],
|
|
28
|
+
"hasJaxKnowledge": NotRequired[bool],
|
|
29
|
+
"transcript_in_jaxckb": NotRequired[bool],
|
|
30
|
+
"cosmic_sample_count": NotRequired[float],
|
|
31
|
+
"class": NotRequired[Union[str, List[str]]],
|
|
32
|
+
"group": NotRequired[Union[str, List[str]]],
|
|
33
|
+
"impact": NotRequired[Union[str, List[str]]],
|
|
34
|
+
"biotype": NotRequired[Union[str, List[str]]],
|
|
35
|
+
"rs_id": NotRequired[Union[str, List[str]]],
|
|
36
|
+
"chromosome": NotRequired[Union[str, List[str]]],
|
|
37
|
+
"clinvar_allele_id": NotRequired[Union[str, List[str]]],
|
|
38
|
+
"clinvar_disease": NotRequired[Union[str, List[str]]],
|
|
39
|
+
"clinvar_review": NotRequired[Union[str, List[str]]],
|
|
40
|
+
"clinvar_significance": NotRequired[Union[str, List[str]]],
|
|
41
|
+
"clinvar_submission": NotRequired[Union[str, List[str]]],
|
|
42
|
+
"transcript_gene": NotRequired[Union[str, List[str]]],
|
|
43
|
+
"transcript_gene_id": NotRequired[Union[str, List[str]]],
|
|
44
|
+
"transcript_classification": NotRequired[Union[str, List[str]]],
|
|
45
|
+
"transcript_group": NotRequired[Union[str, List[str]]],
|
|
46
|
+
"transcript_impact": NotRequired[Union[str, List[str]]],
|
|
47
|
+
"transcript_id": NotRequired[Union[str, List[str]]],
|
|
48
|
+
"transcript_biotype": NotRequired[Union[str, List[str]]],
|
|
49
|
+
"transcript_exon_intron_rank": NotRequired[Union[str, List[str]]],
|
|
50
|
+
"transcript_hgvs_amino_acid_change": NotRequired[Union[str, List[str]]],
|
|
51
|
+
"transcript_nucleotide_change": NotRequired[Union[str, List[str]]],
|
|
52
|
+
"transcript_jax_protein_effect": NotRequired[Union[str, List[str]]],
|
|
53
|
+
"transcript_jax_knowledge": NotRequired[Union[str, List[str]]],
|
|
54
|
+
"cosmic_id": NotRequired[Union[str, List[str]]],
|
|
55
|
+
"cosmic_mutation_status": NotRequired[Union[str, List[str]]],
|
|
56
|
+
"cosmic_histology": NotRequired[Union[str, List[str]]],
|
|
57
|
+
"cosmic_tumor_site": NotRequired[Union[str, List[str]]],
|
|
58
|
+
"dbnsfp_fathmm_pred": NotRequired[Union[str, List[str]]],
|
|
59
|
+
"dbnsfp_mutationtaster_pred": NotRequired[Union[str, List[str]]],
|
|
60
|
+
"dbnsfp_sift_pred": NotRequired[Union[str, List[str]]],
|
|
61
|
+
"sample_zygosity": NotRequired[Union[str, List[str]]],
|
|
62
|
+
"sample_genotype": NotRequired[Union[str, List[str]]],
|
|
63
|
+
"sample_filter": NotRequired[Union[str, List[str]]],
|
|
64
|
+
"sample_vendsig": NotRequired[Union[str, List[str]]],
|
|
65
|
+
"sequence_type": NotRequired[Union[str, List[str]]],
|
|
66
|
+
"position": NotRequired[Union[str, List[str]]],
|
|
67
|
+
"clinvar_near_variant": NotRequired[Union[str, List[str]]],
|
|
68
|
+
"cosmic_near_variant": NotRequired[Union[str, List[str]]],
|
|
69
|
+
"minimum_allele_frequency": NotRequired[Union[str, List[str]]],
|
|
70
|
+
"maximum_allele_frequency": NotRequired[Union[str, List[str]]],
|
|
71
|
+
"population_allele_frequency": NotRequired[Union[str, List[str]]],
|
|
72
|
+
"exac_allele_frequency": NotRequired[Union[str, List[str]]],
|
|
73
|
+
"exac_homozygous": NotRequired[Union[str, List[str]]],
|
|
74
|
+
"dbnsfp_damaging_count": NotRequired[Union[str, List[str]]],
|
|
75
|
+
"dbnsfp_damaging_predictor": NotRequired[Union[str, List[str]]],
|
|
76
|
+
"dbnsfp_damaging_vote": NotRequired[Union[str, List[str]]],
|
|
77
|
+
"dbnsfp_fathmm_rankscore": NotRequired[Union[str, List[str]]],
|
|
78
|
+
"dbnsfp_mean_rankscore": NotRequired[Union[str, List[str]]],
|
|
79
|
+
"dbnsfp_mean_rankscore_predictor": NotRequired[Union[str, List[str]]],
|
|
80
|
+
"dbnsfp_mutationtaster_rankscore": NotRequired[Union[str, List[str]]],
|
|
81
|
+
"dbnsfp_sift_rankscore": NotRequired[Union[str, List[str]]],
|
|
82
|
+
"sample_allele_frequency": NotRequired[Union[str, List[str]]],
|
|
83
|
+
"sample_quality": NotRequired[Union[str, List[str]]],
|
|
84
|
+
"sample_read_depth": NotRequired[Union[str, List[str]]],
|
|
85
|
+
"sample_alternate_read_depth": NotRequired[Union[str, List[str]]],
|
|
86
|
+
"sample_reference_read_depth": NotRequired[Union[str, List[str]]],
|
|
87
|
+
"nextPageToken": NotRequired[str],
|
|
88
|
+
"pageSize": NotRequired[float],
|
|
89
|
+
},
|
|
90
|
+
)
|
|
91
|
+
|
|
92
|
+
|
|
93
|
+
class Clinvar(TypedDict):
|
|
94
|
+
nearVariant: float
|
|
95
|
+
|
|
96
|
+
|
|
97
|
+
class Cosmic(TypedDict):
|
|
98
|
+
sampleCount: float
|
|
99
|
+
nearVariant: float
|
|
100
|
+
tumorSite: NotRequired[str]
|
|
101
|
+
histology: NotRequired[str]
|
|
102
|
+
cosmicId: NotRequired[str]
|
|
103
|
+
status: NotRequired[str]
|
|
104
|
+
|
|
105
|
+
|
|
106
|
+
EnsemblCanonItem = TypedDict(
|
|
107
|
+
"EnsemblCanonItem",
|
|
108
|
+
{
|
|
109
|
+
"class": NotRequired[str],
|
|
110
|
+
"impact": NotRequired[str],
|
|
111
|
+
"gene": NotRequired[str],
|
|
112
|
+
"geneId": NotRequired[str],
|
|
113
|
+
"transcriptId": NotRequired[str],
|
|
114
|
+
"biotype": NotRequired[str],
|
|
115
|
+
"exonIntronRank": NotRequired[str],
|
|
116
|
+
"nucleotideChange": NotRequired[str],
|
|
117
|
+
"aminoAcidChange": NotRequired[str],
|
|
118
|
+
"hgvsAminoAcidChange": NotRequired[str],
|
|
119
|
+
},
|
|
120
|
+
)
|
|
121
|
+
|
|
122
|
+
|
|
123
|
+
class Dbnsfp(TypedDict):
|
|
124
|
+
siftPred: List[Optional[str]]
|
|
125
|
+
mutationTasterPred: List[Optional[str]]
|
|
126
|
+
fathmmPred: List[Optional[str]]
|
|
127
|
+
|
|
128
|
+
|
|
129
|
+
EnsemblItem = TypedDict(
|
|
130
|
+
"EnsemblItem",
|
|
131
|
+
{
|
|
132
|
+
"class": NotRequired[str],
|
|
133
|
+
"impact": NotRequired[str],
|
|
134
|
+
"gene": NotRequired[str],
|
|
135
|
+
"geneId": NotRequired[str],
|
|
136
|
+
"transcriptId": NotRequired[str],
|
|
137
|
+
"biotype": NotRequired[str],
|
|
138
|
+
"exonIntronRank": NotRequired[str],
|
|
139
|
+
"nucleotideChange": NotRequired[str],
|
|
140
|
+
"aminoAcidChange": NotRequired[str],
|
|
141
|
+
"hgvsAminoAcidChange": NotRequired[str],
|
|
142
|
+
},
|
|
143
|
+
)
|
|
144
|
+
|
|
145
|
+
|
|
146
|
+
class Vcf(TypedDict):
|
|
147
|
+
quality: float
|
|
148
|
+
filter: str
|
|
149
|
+
variantAllelicFrequency: float
|
|
150
|
+
coverage: str
|
|
151
|
+
|
|
152
|
+
|
|
153
|
+
class Item(TypedDict):
|
|
154
|
+
id: str
|
|
155
|
+
chromosome: str
|
|
156
|
+
reference: str
|
|
157
|
+
alternate: str
|
|
158
|
+
position: float
|
|
159
|
+
minimumAlleleFrequency: float
|
|
160
|
+
maximumAlleleFrequency: float
|
|
161
|
+
gnomadAlleleFrequency: float
|
|
162
|
+
gnomadHomozygous: float
|
|
163
|
+
rsid: str
|
|
164
|
+
zygosity: str
|
|
165
|
+
clinvar: Clinvar
|
|
166
|
+
cosmic: Cosmic
|
|
167
|
+
ensemblCanon: List[EnsemblCanonItem]
|
|
168
|
+
dbnsfp: Dbnsfp
|
|
169
|
+
ensembl: NotRequired[List[EnsemblItem]]
|
|
170
|
+
vcf: NotRequired[Vcf]
|
|
171
|
+
|
|
172
|
+
|
|
173
|
+
class Links(TypedDict):
|
|
174
|
+
self: str
|
|
175
|
+
next: NotRequired[str]
|
|
176
|
+
|
|
177
|
+
|
|
178
|
+
class Invalid(TypedDict):
|
|
179
|
+
variantSetIds: List[str]
|
|
180
|
+
|
|
181
|
+
|
|
182
|
+
class SearchVariantsResponse(TypedDict):
|
|
183
|
+
items: NotRequired[List[Item]]
|
|
184
|
+
links: Links
|
|
185
|
+
sorted: NotRequired[bool]
|
|
186
|
+
count: NotRequired[float]
|
|
187
|
+
invalid: NotRequired[Invalid]
|
|
188
|
+
|
|
189
|
+
|
|
190
|
+
class GenomicsServiceClient(BaseClient):
|
|
191
|
+
def __init__(self, **cfg: Unpack[AlphaConfig]):
|
|
192
|
+
kwargs = {"target": "lambda://genomics-service:deployed", **(cfg or {})}
|
|
193
|
+
super().__init__(**kwargs)
|
|
194
|
+
|
|
195
|
+
async def search_variants(self, body: SearchVariantsRequest):
|
|
196
|
+
"""Search for variants"""
|
|
197
|
+
res = await self.client.request(
|
|
198
|
+
path="/v1/genomics/variants/_search", method="POST", body=cast(dict, body)
|
|
199
|
+
)
|
|
200
|
+
return cast(AlphaResponse[SearchVariantsResponse], res)
|
|
@@ -13,6 +13,7 @@ fountain_life_service_clients/email_service_sms.py,sha256=6W9Ba0Qj8oRtPMOrMx2HPk
|
|
|
13
13
|
fountain_life_service_clients/fhir_post_processor_service.py,sha256=4IsyyRoCIzSNIBMvJFi1QyFuekikmtoY7ahQCh8Oncw,1355
|
|
14
14
|
fountain_life_service_clients/fhir_search_service.py,sha256=O_y8YrOjvKj_Tfs5Pj4MM4X6RvV1E2s762lRH5U8ji8,6014
|
|
15
15
|
fountain_life_service_clients/file_service.py,sha256=CY36fpvCAi17npAKAWkFDDaNhwbvTC5hx-sGZmPfyBM,4046
|
|
16
|
+
fountain_life_service_clients/genomics_service.py,sha256=uigsDX5C98i7kvWFmEf7dyWQIMi0g1g4D72epri1QGg,7368
|
|
16
17
|
fountain_life_service_clients/invitation_service.py,sha256=tKWgb-bGIwT4x3MWSLiVChQRaZURj43S6Uyrg3Lt7HA,2596
|
|
17
18
|
fountain_life_service_clients/medical_results_service_results.py,sha256=L0clTifU4LWWKgBsIzEfelmkaICxG1_q8sHyrdA5es4,4876
|
|
18
19
|
fountain_life_service_clients/member_notification_service.py,sha256=wRkgmUqAV59BV81c3Iwz7JxSTuOLagHrcJcXvMbdBco,1814
|
|
@@ -24,6 +25,6 @@ fountain_life_service_clients/rules_service.py,sha256=VxPYboYQmw--6Kn78RKu6_9as1
|
|
|
24
25
|
fountain_life_service_clients/scheduler_service.py,sha256=IkwRns_QHh6fx1IZWEXZ35DeRiW7OHaROM5wjWubZm4,4440
|
|
25
26
|
fountain_life_service_clients/survey_service.py,sha256=hxOl3gBDxEdjrsKcMCoPl9RxumQzRT-e4zTbEAA0Iq4,13343
|
|
26
27
|
fountain_life_service_clients/user_service.py,sha256=rM9xcF-VzdLp9aDOhg1UbecX2VPPMxH9PlgpNpGdC18,4253
|
|
27
|
-
fountain_life_service_clients-3.
|
|
28
|
-
fountain_life_service_clients-3.
|
|
29
|
-
fountain_life_service_clients-3.
|
|
28
|
+
fountain_life_service_clients-3.31.0.dist-info/METADATA,sha256=m6F4A-ihb2vKerjPmgl80oD5e0Wk3g_hZlrpc8pU3iU,1405
|
|
29
|
+
fountain_life_service_clients-3.31.0.dist-info/WHEEL,sha256=M5asmiAlL6HEcOq52Yi5mmk9KmTVjY2RDPtO4p9DMrc,88
|
|
30
|
+
fountain_life_service_clients-3.31.0.dist-info/RECORD,,
|
|
File without changes
|