fix: update cool-seq-tool to 0.1.13 (#410)

* fix: update cool-seq-tool to 0.1.13 - MANE Summary data >= v1.1 uses NC accessions for GRCh38_chr now * refactor: parsed_to_cn_var warning message (#411) - "assembly is not current supported" --> "assembly is not currently supported"
cancervariants · May 2, 2023 · 647b29d · 647b29d
1 parent 668140b
commit 647b29d
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diff --git a/Pipfile b/Pipfile
@@ -28,5 +28,5 @@ gene-normalizer = ">=0.2.9"
 pyliftover = "*"
 boto3 = "*"
 "ga4gh.vrsatile.pydantic" = ">=0.1.0.dev8, < 0.2.0"
-cool-seq-tool = ">=0.1.12"
+cool-seq-tool = ">=0.1.13"
 bioutils = "*"
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -13,8 +13,8 @@ beautifulsoup4==4.12.2 ; python_full_version >= '3.6.0'
 biocommons.seqrepo==0.6.5
 bioutils==0.5.7
 bleach==6.0.0 ; python_version >= '3.7'
-boto3==1.26.115
-botocore==1.29.115 ; python_version >= '3.7'
+boto3==1.26.123
+botocore==1.29.123 ; python_version >= '3.7'
 bs4==0.0.1
 canonicaljson==2.0.0 ; python_version >= '3.7'
 certifi==2022.12.7 ; python_version >= '3.6'
@@ -25,8 +25,8 @@ click==8.1.3 ; python_version >= '3.7'
 coloredlogs==15.0.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 comm==0.1.3 ; python_version >= '3.6'
 configparser==5.3.0 ; python_version >= '3.7'
-cool-seq-tool==0.1.12
-coverage[toml]==7.2.3 ; python_version >= '3.7'
+cool-seq-tool==0.1.13
+coverage[toml]==7.2.5 ; python_version >= '3.7'
 cssselect==1.2.0 ; python_version >= '3.7'
 cython==0.29.34 ; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'
 debugpy==1.6.7 ; python_version >= '3.7'
@@ -49,13 +49,13 @@ gene-normalizer==0.2.9
 h11==0.14.0 ; python_version >= '3.7'
 hgvs==1.5.4 ; python_version >= '3.6'
 humanfriendly==10.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-identify==2.5.22 ; python_version >= '3.7'
+identify==2.5.23 ; python_version >= '3.7'
 idna==3.4 ; python_version >= '3.5'
-importlib-metadata==6.5.0 ; python_version >= '3.7'
+importlib-metadata==6.6.0 ; python_version >= '3.7'
 inflection==0.5.1 ; python_version >= '3.5'
 iniconfig==2.0.0 ; python_version >= '3.7'
 ipykernel==6.22.0
-ipython==8.12.0 ; python_version >= '3.8'
+ipython==8.13.1 ; python_version >= '3.9'
 ipython-genutils==0.2.0
 ipywidgets==8.0.6 ; python_version >= '3.7'
 jedi==0.18.2 ; python_version >= '3.6'
@@ -77,24 +77,24 @@ markupsafe==2.1.2 ; python_version >= '3.7'
 matplotlib-inline==0.1.6 ; python_version >= '3.5'
 mccabe==0.7.0 ; python_version >= '3.6'
 mistune==2.0.5
-nbclassic==0.5.5 ; python_version >= '3.7'
-nbclient==0.7.3 ; python_full_version >= '3.7.0'
+nbclassic==0.5.6 ; python_version >= '3.7'
+nbclient==0.7.4 ; python_full_version >= '3.7.0'
 nbconvert==7.3.1 ; python_version >= '3.7'
 nbformat==5.8.0 ; python_version >= '3.7'
 nest-asyncio==1.5.6 ; python_version >= '3.5'
 nodeenv==1.7.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6'
 notebook==6.5.4 ; python_version >= '3.7'
-notebook-shim==0.2.2 ; python_version >= '3.7'
-numpy==1.24.2 ; python_version >= '3.8'
+notebook-shim==0.2.3 ; python_version >= '3.7'
+numpy==1.24.3 ; python_version >= '3.8'
 packaging==23.1 ; python_version >= '3.7'
-pandas==2.0.0 ; python_version >= '3.8'
+pandas==2.0.1 ; python_version >= '3.8'
 pandocfilters==1.5.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 parse==1.19.0
 parsley==1.3
 parso==0.8.3 ; python_version >= '3.6'
 pexpect==4.8.0 ; sys_platform != 'win32'
 pickleshare==0.7.5
-platformdirs==3.2.0 ; python_version >= '3.7'
+platformdirs==3.5.0 ; python_version >= '3.7'
 pluggy==1.0.0 ; python_version >= '3.6'
 pre-commit==3.2.2
 prometheus-client==0.16.0 ; python_version >= '3.6'
@@ -127,13 +127,13 @@ pyyaml==6.0 ; python_version >= '3.6'
 pyzmq==25.0.2 ; python_version >= '3.6'
 qtconsole==5.4.2 ; python_version >= '3.7'
 qtpy==2.3.1 ; python_version >= '3.7'
-requests==2.28.2 ; python_version >= '3.7' and python_version < '4'
+requests==2.29.0 ; python_version >= '3.7'
 requests-html==0.10.0 ; python_full_version >= '3.6.0'
 rfc3339-validator==0.1.4 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 rfc3986-validator==0.1.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 s3transfer==0.6.0 ; python_version >= '3.7'
-send2trash==1.8.0
-setuptools==67.6.1 ; python_version >= '3.7'
+send2trash==1.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+setuptools==67.7.2 ; python_version >= '3.7'
 six==1.16.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
 sniffio==1.3.0 ; python_version >= '3.7'
 snowballstemmer==2.2.0
@@ -144,15 +144,15 @@ starlette==0.26.1 ; python_version >= '3.7'
 tabulate==0.9.0 ; python_version >= '3.7'
 terminado==0.17.1 ; python_version >= '3.7'
 tinycss2==1.2.1 ; python_version >= '3.7'
-tornado==6.3 ; python_version >= '3.8'
+tornado==6.3.1 ; python_version >= '3.8'
 tqdm==4.65.0 ; python_version >= '3.7'
 traitlets==5.9.0 ; python_version >= '3.7'
 typing-extensions==4.5.0 ; python_version >= '3.7'
 tzdata==2023.3 ; python_version >= '2'
 urllib3==1.26.15 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
-uvicorn==0.21.1
+uvicorn==0.22.0
 -e .
-virtualenv==20.21.0 ; python_version >= '3.7'
+virtualenv==20.23.0 ; python_version >= '3.7'
 w3lib==2.1.1 ; python_version >= '3.7'
 wcwidth==0.2.6
 webencodings==0.5.1

diff --git a/requirements.txt b/requirements.txt
@@ -10,16 +10,16 @@ backcall==0.2.0
 beautifulsoup4==4.12.2 ; python_full_version >= '3.6.0'
 biocommons.seqrepo==0.6.5
 bioutils==0.5.7
-boto3==1.26.115
-botocore==1.29.115 ; python_version >= '3.7'
+boto3==1.26.123
+botocore==1.29.123 ; python_version >= '3.7'
 bs4==0.0.1
 canonicaljson==2.0.0 ; python_version >= '3.7'
 certifi==2022.12.7 ; python_version >= '3.6'
 charset-normalizer==3.1.0 ; python_full_version >= '3.7.0'
 click==8.1.3 ; python_version >= '3.7'
 coloredlogs==15.0.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 configparser==5.3.0 ; python_version >= '3.7'
-cool-seq-tool==0.1.12
+cool-seq-tool==0.1.13
 cssselect==1.2.0 ; python_version >= '3.7'
 cython==0.29.34 ; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'
 decorator==5.1.1 ; python_version >= '3.5'
@@ -33,17 +33,17 @@ h11==0.14.0 ; python_version >= '3.7'
 hgvs==1.5.4 ; python_version >= '3.6'
 humanfriendly==10.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 idna==3.4 ; python_version >= '3.5'
-importlib-metadata==6.5.0 ; python_version >= '3.7'
+importlib-metadata==6.6.0 ; python_version >= '3.7'
 inflection==0.5.1 ; python_version >= '3.5'
-ipython==8.12.0 ; python_version >= '3.8'
+ipython==8.13.1 ; python_version >= '3.9'
 jedi==0.18.2 ; python_version >= '3.6'
 jmespath==1.0.1 ; python_version >= '3.7'
 jsonschema==3.2.0
 lxml==4.9.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 markdown==3.4.3 ; python_version >= '3.7'
 matplotlib-inline==0.1.6 ; python_version >= '3.5'
-numpy==1.24.2 ; python_version >= '3.8'
-pandas==2.0.0 ; python_version >= '3.8'
+numpy==1.24.3 ; python_version >= '3.8'
+pandas==2.0.1 ; python_version >= '3.8'
 parse==1.19.0
 parsley==1.3
 parso==0.8.3 ; python_version >= '3.6'
@@ -66,10 +66,10 @@ python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0,
 python-jsonschema-objects==0.4.1
 pytz==2023.3
 pyyaml==6.0 ; python_version >= '3.6'
-requests==2.28.2 ; python_version >= '3.7' and python_version < '4'
+requests==2.29.0 ; python_version >= '3.7'
 requests-html==0.10.0 ; python_full_version >= '3.6.0'
 s3transfer==0.6.0 ; python_version >= '3.7'
-setuptools==67.6.1 ; python_version >= '3.7'
+setuptools==67.7.2 ; python_version >= '3.7'
 six==1.16.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'
 sniffio==1.3.0 ; python_version >= '3.7'
 soupsieve==2.4.1 ; python_version >= '3.7'
@@ -82,7 +82,7 @@ traitlets==5.9.0 ; python_version >= '3.7'
 typing-extensions==4.5.0 ; python_version >= '3.7'
 tzdata==2023.3 ; python_version >= '2'
 urllib3==1.26.15 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
-uvicorn==0.21.1
+uvicorn==0.22.0
 w3lib==2.1.1 ; python_version >= '3.7'
 wcwidth==0.2.6
 websockets==10.4 ; python_version >= '3.7'

diff --git a/setup.cfg b/setup.cfg
@@ -34,7 +34,7 @@ install_requires =
     pyliftover
     boto3
     ga4gh.vrsatile.pydantic >= 0.1.0.dev8, < 0.2.0
-    cool-seq-tool >= 0.1.12
+    cool-seq-tool >= 0.1.13
     bioutils
 
 tests_require =

diff --git a/tests/test_gnomad_vcf_to_protein.py b/tests/test_gnomad_vcf_to_protein.py
@@ -852,10 +852,6 @@ async def test_invalid(test_handler):
     assert resp.variation_descriptor.label == "7-140753336-T-G"
     assert set(resp.warnings) == {
         "Expected T but found A on NC_000007.14 at position 140753336",
-        "Unable to get MANE data for NM_004333.6 using NC_000007.13 at positions"
-        " 140753335 to 140753335",  # MANE Select
-        "Unable to get MANE data for NM_001374258.1 using NC_000007.13 at positions"
-        " 140753335 to 140753335"  # MANE Plus Clinical
     }
 
     resp = await test_handler.gnomad_vcf_to_protein("20-2-TC-TG",

diff --git a/tests/to_copy_number_variation/test_parsed_to_cn_var.py b/tests/to_copy_number_variation/test_parsed_to_cn_var.py
@@ -203,7 +203,7 @@ def test_invalid(test_cnv_handler):
     """Test invalid queries returns Text variation and warnings"""
     # NCBI36/hg18 assembly
     # https://www.ncbi.nlm.nih.gov/clinvar/variation/443961/?new_evidence=true
-    expected_w = ["NCBI36 assembly is not current supported"]
+    expected_w = ["NCBI36 assembly is not currently supported"]
     resp = test_cnv_handler.parsed_to_cn_var(
         2623228, 3150942, 3, assembly=ClinVarAssembly.NCBI36, chr="chr1",
         untranslatable_returns_text=True)

diff --git a/variation/gnomad_vcf_to_protein_variation.py b/variation/gnomad_vcf_to_protein_variation.py
@@ -294,9 +294,8 @@ async def gnomad_vcf_to_protein(
                         )
                         continue
 
-                    chromosome = q.split("-")[:-1][0]
                     mane_data = self.mane_transcript_mappings.get_mane_data_from_chr_pos(  # noqa: E501
-                        chromosome, g_start_pos, g_end_pos)
+                        alt_ac, g_start_pos, g_end_pos)
                     mane_data_len = len(mane_data)
                     g_start_pos -= 1
                     g_end_pos -= 1

diff --git a/variation/to_copy_number_variation.py b/variation/to_copy_number_variation.py
@@ -231,7 +231,7 @@ def parsed_to_cn_var(
                         if not accession:
                             warnings.append(f"Unable to find RefSeq accession for {query}")  # noqa: E501
                 else:
-                    warnings.append(f"{assembly.value} assembly is not current supported")  # noqa: E501
+                    warnings.append(f"{assembly.value} assembly is not currently supported")  # noqa: E501
             else:
                 warnings.append("Must provide either `accession` or both `assembly` "
                                 "and `chr`.")

diff --git a/variation/version.py b/variation/version.py
@@ -1 +1 @@
-__version__ = "0.7.0-dev6"
+__version__ = "0.7.0-dev7"