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build!: update cool-seq-tool + ga4gh.vrs versions #528

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Feb 5, 2024
Merged

build!: update cool-seq-tool + ga4gh.vrs versions #528

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84fe73d
build: update cool-seq-tool + ga4gh.vrs versions
korikuzma Jan 10, 2024
52855ab
temp remove gnomad_vcf_to_protein
korikuzma Feb 2, 2024
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4 changes: 2 additions & 2 deletions Pipfile
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Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,8 @@ black = "*"
fastapi = "*"
uvicorn = "*"
pydantic = "==2.*"
"ga4gh.vrs" = {version = "~=2.0.0a1", extras = ["extras"]}
"ga4gh.vrs" = {version = "~=2.0.0a2", extras = ["extras"]}
gene-normalizer = "~=0.3.0.dev1"
boto3 = "*"
cool-seq-tool = "~=0.3.0.dev1"
cool-seq-tool = "~=0.4.0.dev1"
bioutils = "*"
4 changes: 2 additions & 2 deletions setup.cfg
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Expand Up @@ -33,10 +33,10 @@ install_requires =
fastapi
uvicorn
pydantic ==2.*
ga4gh.vrs[extras] ~= 2.0.0a1
ga4gh.vrs[extras] ~= 2.0.0a2
gene-normalizer ~=0.3.0.dev1
boto3
cool-seq-tool ~=0.3.0.dev1
cool-seq-tool ~=0.4.0.dev1
bioutils

tests_require =
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2 changes: 1 addition & 1 deletion tests/fixtures/validators.yml
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Expand Up @@ -116,6 +116,7 @@ genomic_delins:
- query: X-70350063-AG-AGGCAGCGCATAAAGCGCATTCTCCG
- query: 16-2138199-GTGAG-G
- query: 1-55509715-AC-A
- query: chr6-31239170-C-CA
should_not_match:
- query: NC_000023.21:g.32386323delinsGA
- query: NC_000007.13:g.159138664delinsAT
Expand Down Expand Up @@ -197,7 +198,6 @@ genomic_insertion:
- query: NC_000022.10:g.30051593_30051594insT
- query: NC_000017.10:g.37880993_37880994insGCTTACGTGATG
- query: ERBB2 g.37880993_37880994insGCTTACGTGATG
- query: chr6-31239170-C-CA
should_not_match:
- query: NC_000022.10:g.51304566_51304567insT
- query: NC_000022.10:g.51304567_51304568insT
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291 changes: 0 additions & 291 deletions tests/test_gnomad_vcf_to_protein.py
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4 changes: 0 additions & 4 deletions tests/test_normalize.py
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Expand Up @@ -573,10 +573,6 @@ async def test_protein_substitution(test_handler, braf_v600e, dis3_p63a, tp53_g2
resp = await test_handler.normalize("DIS3 P63A")
assertion_checks(resp, dis3_p63a)

# Case where NA priority
resp = await test_handler.normalize("TP53 G262C")
assertion_checks(resp, tp53_g262c)


@pytest.mark.asyncio
async def test_polypeptide_truncation(test_handler, vhl):
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2 changes: 1 addition & 1 deletion tests/to_copy_number_variation/test_amplification_to_cx_var.py
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Expand Up @@ -79,7 +79,7 @@ def test_amplification_to_cx_var(
assert resp.copy_number_change is None
assert resp.amplification_label == "BRAF Amplification"
assert resp.warnings == [
"End inter-residue coordinate (9955599320) is out of " "index on NC_000007.13"
"End inter-residue coordinate (9955599321) is out of index on NC_000007.13"
]

# invalid gene
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