From 647b29d7a67501bfda99cbd04f31ba7d2a102587 Mon Sep 17 00:00:00 2001 From: Kori Kuzma Date: Tue, 2 May 2023 07:25:42 -0400 Subject: [PATCH] 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" --- Pipfile | 2 +- requirements-dev.txt | 38 +++++++++---------- requirements.txt | 20 +++++----- setup.cfg | 2 +- tests/test_gnomad_vcf_to_protein.py | 4 -- .../test_parsed_to_cn_var.py | 2 +- variation/gnomad_vcf_to_protein_variation.py | 3 +- variation/to_copy_number_variation.py | 2 +- variation/version.py | 2 +- 9 files changed, 35 insertions(+), 40 deletions(-) diff --git a/Pipfile b/Pipfile index e863c71c..9ac0cc8c 100644 --- 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 index 7658ed44..9485bcdb 100644 --- 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 index 4eb8db66..123d9df7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,8 +10,8 @@ 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' @@ -19,7 +19,7 @@ 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 index 1d8cb603..d681a0ce 100644 --- 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 index 5a05495d..d49bc0bd 100644 --- 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 index 4ba1c347..17b2fb0d 100644 --- 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 index 49e65dbb..0de16c41 100644 --- 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 index 01b09764..d24840fc 100644 --- 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 index 28d371d5..82665a2c 100644 --- a/variation/version.py +++ b/variation/version.py @@ -1 +1 @@ -__version__ = "0.7.0-dev6" +__version__ = "0.7.0-dev7"