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Add tests for ComposedSequenceExpression (#408) #413

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merged 2 commits into from
Jan 16, 2023
Merged

Add tests for ComposedSequenceExpression (#408) #413

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55d0859
Add tests for ComposedSequenceExpression (#408)
korikuzma Nov 14, 2022
5e6976b
Merge branch 'main' into issue-408
korikuzma Jan 16, 2023
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94 changes: 94 additions & 0 deletions validation/models.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -169,6 +169,38 @@ RepeatedSequenceExpression:
type: RepeatedSequenceExpression
out:
ga4gh_serialize: '{"count":{"comparator":">=","type":"IndefiniteRange","value":6},"seq_expr":{"location":"QrRSuBj-VScAGV_gEdxNgsnh41jYH1Kg","reverse_complement":false,"type":"DerivedSequenceExpression"},"type":"RepeatedSequenceExpression"}'
ComposedSequenceExpression:
- name: "Composed Sequence Expression w/ order 1"
in:
components:
- type: LiteralSequenceExpression
sequence: CGC
- type: RepeatedSequenceExpression
seq_expr:
type: LiteralSequenceExpression
sequence: CGA
count:
type: Number
value: 3
type: ComposedSequenceExpression
out:
ga4gh_serialize: '{"components":[{"sequence":"CGC","type":"LiteralSequenceExpression"},{"count":{"type":"Number","value":3},"seq_expr":{"sequence":"CGA","type":"LiteralSequenceExpression"},"type":"RepeatedSequenceExpression"}],"type":"ComposedSequenceExpression"}'
ComposedSequenceExpression:
- name: "Composed Sequence Expression w/ order 2"
in:
components:
- type: RepeatedSequenceExpression
seq_expr:
type: LiteralSequenceExpression
sequence: CGA
count:
type: Number
value: 3
- type: LiteralSequenceExpression
sequence: CGC
type: ComposedSequenceExpression
out:
ga4gh_serialize: '{"components":[{"count":{"type":"Number","value":3},"seq_expr":{"sequence":"CGA","type":"LiteralSequenceExpression"},"type":"RepeatedSequenceExpression"},{"sequence":"CGC","type":"LiteralSequenceExpression"}],"type":"ComposedSequenceExpression"}'
Allele:
- name: "rs7412@GRCh38>T w/SequenceState"
in:
Expand Down Expand Up @@ -213,6 +245,68 @@ Allele:
ga4gh_digest: CxiA_hvYbkD8Vqwjhx5AYuyul4mtlkpD
ga4gh_identify: ga4gh:VA.CxiA_hvYbkD8Vqwjhx5AYuyul4mtlkpD
ga4gh_serialize: '{"location":"QrRSuBj-VScAGV_gEdxNgsnh41jYH1Kg","state":{"sequence":"T","type":"LiteralSequenceExpression"},"type":"Allele"}'
Allele:
- name: "Allele w/ Composed Sequence Expression w/ order 1"
in:
location:
interval:
end:
type: Number
value: 44908822
start:
type: Number
value: 44908821
type: SequenceInterval
sequence_id: ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl
type: SequenceLocation
state:
components:
- type: LiteralSequenceExpression
sequence: CGC
- type: RepeatedSequenceExpression
seq_expr:
type: LiteralSequenceExpression
sequence: CGA
count:
type: Number
value: 3
type: ComposedSequenceExpression
type: Allele
out:
ga4gh_digest: obWIAB54mfRE2HAwQiIzKZeIx0REPG-8
ga4gh_identify: ga4gh:VA.obWIAB54mfRE2HAwQiIzKZeIx0REPG-8
ga4gh_serialize: '{"location":"QrRSuBj-VScAGV_gEdxNgsnh41jYH1Kg","state":{"components":[{"sequence":"CGC","type":"LiteralSequenceExpression"},{"count":{"type":"Number","value":3},"seq_expr":{"sequence":"CGA","type":"LiteralSequenceExpression"},"type":"RepeatedSequenceExpression"}],"type":"ComposedSequenceExpression"},"type":"Allele"}'
Allele:
- name: "Allele w/ Composed Sequence Expression w/ order 2"
in:
location:
interval:
end:
type: Number
value: 44908822
start:
type: Number
value: 44908821
type: SequenceInterval
sequence_id: ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl
type: SequenceLocation
state:
components:
- type: RepeatedSequenceExpression
seq_expr:
type: LiteralSequenceExpression
sequence: CGA
count:
type: Number
value: 3
- type: LiteralSequenceExpression
sequence: CGC
type: ComposedSequenceExpression
type: Allele
out:
ga4gh_digest: KDrbvmR-Y2dccsgckQnpEsQuLMq4p10d
ga4gh_identify: ga4gh:VA.KDrbvmR-Y2dccsgckQnpEsQuLMq4p10d
ga4gh_serialize: '{"location":"QrRSuBj-VScAGV_gEdxNgsnh41jYH1Kg","state":{"components":[{"count":{"type":"Number","value":3},"seq_expr":{"sequence":"CGA","type":"LiteralSequenceExpression"},"type":"RepeatedSequenceExpression"},{"sequence":"CGC","type":"LiteralSequenceExpression"}],"type":"ComposedSequenceExpression"},"type":"Allele"}'
Haplotype:
- name: "APOE1 on GRCh38, inline"
in:
Expand Down