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

* Updates cool-seq-tool + ga4gh.vrs versions. This mainly had to do with fixing inter-residue positions. cool-seq-tool previous versions returned 0-based coordinates. * Temporarily removes gnomad_vcf_to_protein, which will be added back in #529
cancervariants · Feb 5, 2024 · 156ebeb · 156ebeb
1 parent e0a7709
commit 156ebeb
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Showing 30 changed files with 157 additions and 995 deletions.
diff --git a/Pipfile b/Pipfile
@@ -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 = "*"
diff --git a/setup.cfg b/setup.cfg
@@ -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 =

diff --git a/tests/fixtures/validators.yml b/tests/fixtures/validators.yml
@@ -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
@@ -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

diff --git a/tests/test_gnomad_vcf_to_protein.py b/tests/test_gnomad_vcf_to_protein.py
diff --git a/tests/test_normalize.py b/tests/test_normalize.py
@@ -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):

diff --git a/tests/to_copy_number_variation/test_amplification_to_cx_var.py b/tests/to_copy_number_variation/test_amplification_to_cx_var.py
@@ -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