From 191f8096eb7864dacbef37d6bf6b7f3938c6ad20 Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Mon, 27 Nov 2023 13:06:28 -0500 Subject: [PATCH 1/2] add examples from https://github.com/ga4gh/vrs/issues/426#issuecomment-1557641780 --- examples/SPDI_contraction.yaml | 16 ++++++++++++++++ examples/SPDI_expansion.yaml | 16 ++++++++++++++++ tests/test_definitions.yaml | 8 ++++++++ 3 files changed, 40 insertions(+) create mode 100644 examples/SPDI_contraction.yaml create mode 100644 examples/SPDI_expansion.yaml diff --git a/examples/SPDI_contraction.yaml b/examples/SPDI_contraction.yaml new file mode 100644 index 00000000..35dd2f82 --- /dev/null +++ b/examples/SPDI_contraction.yaml @@ -0,0 +1,16 @@ +type: Allele +expressions: + - syntax: spdi + value: NC_000001.11:40819438:CTCCTCCT:CTCCT +location: + type: SequenceLocation + sequenceReference: + refgetAccession: ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO + residueAlphabet: na + id: NC_000001.11 + start: 40819438 + end: 40819446 +state: + type: ReferenceLengthExpression + length: 5 + repeatSubunitLength: 3 diff --git a/examples/SPDI_expansion.yaml b/examples/SPDI_expansion.yaml new file mode 100644 index 00000000..acab139e --- /dev/null +++ b/examples/SPDI_expansion.yaml @@ -0,0 +1,16 @@ +type: Allele +expressions: + - syntax: spdi + value: NC_000001.11:40819438:CTCCTCCT:CTCCTCCTCCT +location: + type: SequenceLocation + sequenceReference: + refgetAccession: ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO + residueAlphabet: na + id: NC_000001.11 + start: 40819438 + end: 40819446 +state: + type: ReferenceLengthExpression + length: 11 + repeatSubunitLength: 3 \ No newline at end of file diff --git a/tests/test_definitions.yaml b/tests/test_definitions.yaml index 1334bc2e..10e18e73 100644 --- a/tests/test_definitions.yaml +++ b/tests/test_definitions.yaml @@ -31,3 +31,11 @@ tests: description: A haplotype of two alleles on a shared chromosome reference sequence. schema: vrs definition: Haplotype + - test_file: SPDI_contraction.yaml + description: A simple RLE contraction from SPDI representation + schema: vrs + definition: Allele + - test_file: SPDI_expansion.yaml + description: A simple RLE expansion from SPDI representation + schema: vrs + definition: Allele From 51ab262394757e232bd22ad43cec6f9309da34ef Mon Sep 17 00:00:00 2001 From: "Alex H. Wagner, PhD" Date: Sat, 16 Dec 2023 18:47:32 -0500 Subject: [PATCH 2/2] remove ga4gh namespace from refget accession examples --- examples/SPDI_contraction.yaml | 2 +- examples/SPDI_expansion.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/SPDI_contraction.yaml b/examples/SPDI_contraction.yaml index 35dd2f82..cec43fa3 100644 --- a/examples/SPDI_contraction.yaml +++ b/examples/SPDI_contraction.yaml @@ -5,7 +5,7 @@ expressions: location: type: SequenceLocation sequenceReference: - refgetAccession: ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO + refgetAccession: SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO residueAlphabet: na id: NC_000001.11 start: 40819438 diff --git a/examples/SPDI_expansion.yaml b/examples/SPDI_expansion.yaml index acab139e..243f8d97 100644 --- a/examples/SPDI_expansion.yaml +++ b/examples/SPDI_expansion.yaml @@ -5,7 +5,7 @@ expressions: location: type: SequenceLocation sequenceReference: - refgetAccession: ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO + refgetAccession: SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO residueAlphabet: na id: NC_000001.11 start: 40819438