From e8ccea9aa3278ef822c75c417f8cffde3579d39c Mon Sep 17 00:00:00 2001 From: Alejandro Gonzales-Irribarren Date: Mon, 29 Jul 2024 12:47:40 -0500 Subject: [PATCH] BREAKING CHANGE: GenomeInfo -> AssemblyInfo migration (#6) --- README.md | 2 +- {genomeinfo => assemblyinfo}/__init__.py | 12 +++---- {genomeinfo => assemblyinfo}/build/build.py | 0 {genomeinfo => assemblyinfo}/build/schema.py | 0 {genomeinfo => assemblyinfo}/core/__init__.py | 4 +-- {genomeinfo => assemblyinfo}/core/acc.py | 8 ++--- {genomeinfo => assemblyinfo}/core/assembly.py | 12 +++---- {genomeinfo => assemblyinfo}/core/chrom.py | 10 +++--- {genomeinfo => assemblyinfo}/core/info.py | 34 +++++++++--------- {genomeinfo => assemblyinfo}/data/db.parquet | Bin {genomeinfo => assemblyinfo}/data/init_db.tsv | 0 {genomeinfo => assemblyinfo}/interface.py | 6 ++-- docs/conf.py | 4 +-- docs/index.rst | 8 ++--- docs/quickstart.md | 6 ++-- pyproject.toml | 20 +++++------ tests/test_core_acc.py | 10 +++--- tests/test_core_assembly.py | 10 +++--- tests/test_core_chrom.py | 10 +++--- tests/test_core_info.py | 22 ++++++------ 20 files changed, 89 insertions(+), 89 deletions(-) rename {genomeinfo => assemblyinfo}/__init__.py (53%) rename {genomeinfo => assemblyinfo}/build/build.py (100%) rename {genomeinfo => assemblyinfo}/build/schema.py (100%) rename {genomeinfo => assemblyinfo}/core/__init__.py (96%) rename {genomeinfo => assemblyinfo}/core/acc.py (94%) rename {genomeinfo => assemblyinfo}/core/assembly.py (92%) rename {genomeinfo => assemblyinfo}/core/chrom.py (95%) rename {genomeinfo => assemblyinfo}/core/info.py (93%) rename {genomeinfo => assemblyinfo}/data/db.parquet (100%) rename {genomeinfo => assemblyinfo}/data/init_db.tsv (100%) rename {genomeinfo => assemblyinfo}/interface.py (84%) diff --git a/README.md b/README.md index 87a5fb9..87d582a 100644 --- a/README.md +++ b/README.md @@ -1 +1 @@ -# genomeinfo +# assemblyinfo diff --git a/genomeinfo/__init__.py b/assemblyinfo/__init__.py similarity index 53% rename from genomeinfo/__init__.py rename to assemblyinfo/__init__.py index e10b202..f80d5b2 100644 --- a/genomeinfo/__init__.py +++ b/assemblyinfo/__init__.py @@ -1,20 +1,20 @@ from __future__ import annotations from . import core -from .interface import GenomeInfo +from .interface import AssemblyInfo for module in [core]: for name, func in module.__dict__.items(): if callable(func) and not name.startswith("_"): - setattr(GenomeInfo, name, func) + setattr(AssemblyInfo, name, func) -__all__ = ["GenomeInfo"] +__all__ = ["AssemblyInfo"] -_db: GenomeInfo | None = None +_db: AssemblyInfo | None = None -def connect() -> GenomeInfo: +def connect() -> AssemblyInfo: global _db if _db is None: - _db = GenomeInfo() + _db = AssemblyInfo() return _db diff --git a/genomeinfo/build/build.py b/assemblyinfo/build/build.py similarity index 100% rename from genomeinfo/build/build.py rename to assemblyinfo/build/build.py diff --git a/genomeinfo/build/schema.py b/assemblyinfo/build/schema.py similarity index 100% rename from genomeinfo/build/schema.py rename to assemblyinfo/build/schema.py diff --git a/genomeinfo/core/__init__.py b/assemblyinfo/core/__init__.py similarity index 96% rename from genomeinfo/core/__init__.py rename to assemblyinfo/core/__init__.py index 2410d89..eca83ab 100644 --- a/genomeinfo/core/__init__.py +++ b/assemblyinfo/core/__init__.py @@ -5,7 +5,7 @@ get_refseq_accession, ) from .assembly import ( - AssemblyInfo, + Assembly, assembly_info, ) from .chrom import ( @@ -52,6 +52,6 @@ "get_chromsizes", "get_chrom_eq", "get_seqinfo", - "AssemblyInfo", + "Assembly", "assembly_info", ] diff --git a/genomeinfo/core/acc.py b/assemblyinfo/core/acc.py similarity index 94% rename from genomeinfo/core/acc.py rename to assemblyinfo/core/acc.py index 77612e8..89acf46 100644 --- a/genomeinfo/core/acc.py +++ b/assemblyinfo/core/acc.py @@ -29,7 +29,7 @@ def get_genbank_accession(cls, patch: str) -> str: Examples -------- - >>> GenomeInfo.get_genbank_accession("GRCh38.p14") + >>> AssemblyInfo.get_genbank_accession("GRCh38.p14") """ if not patch: raise ValueError("ERROR: you must provide a patch!") @@ -60,7 +60,7 @@ def get_refseq_accession(cls, patch: str) -> str: Examples -------- - >>> GenomeInfo.get_refseq_accession("GRCh38.p14") + >>> AssemblyInfo.get_refseq_accession("GRCh38.p14") """ if not patch: raise ValueError("ERROR: you must provide a patch!") @@ -91,7 +91,7 @@ def get_patch_from_accession(cls, accession: str) -> List[str]: Examples -------- - >>> GenomeInfo.get_patch_from_accession("GCA_000001405.29") + >>> AssemblyInfo.get_patch_from_accession("GCA_000001405.29") """ if not accession: raise ValueError("ERROR: you must provide an accession!") @@ -130,7 +130,7 @@ def get_assembly_from_accession(cls, accession: str) -> List[str]: Examples -------- - >>> GenomeInfo.get_assembly_from_accession("GCA_000001405.29") + >>> AssemblyInfo.get_assembly_from_accession("GCA_000001405.29") """ if not accession: raise ValueError("ERROR: you must provide an accession!") diff --git a/genomeinfo/core/assembly.py b/assemblyinfo/core/assembly.py similarity index 92% rename from genomeinfo/core/assembly.py rename to assemblyinfo/core/assembly.py index a82bea9..1b5b9e1 100644 --- a/genomeinfo/core/assembly.py +++ b/assemblyinfo/core/assembly.py @@ -6,11 +6,11 @@ from .chrom import filter_chromosome_data from .info import get_assembly_metadata -__all__ = ["AssemblyInfo", "assembly_info"] +__all__ = ["Assembly", "assembly_info"] @dataclass -class AssemblyInfo: +class Assembly: """ A dataclass to store assembly information. """ @@ -35,7 +35,7 @@ def chromeq(self) -> Dict[str, Dict[str, str]]: return pd.DataFrame(self.aliases).T def __repr__(self): - return (f"AssemblyInfo(assembly={self.assembly}", + return (f"Assembly(assembly={self.assembly}", f"species={self.species}", f"common_name={self.common_name})") @@ -47,7 +47,7 @@ def assembly_info( roles: Optional[List[str]] = None, units: Optional[List[str]] = None, length: Optional[str] = None, -) -> AssemblyInfo: +) -> Assembly: """ Get assembly information for a given assembly. Parameters @@ -64,7 +64,7 @@ def assembly_info( Chromosome length. Returns ------- - AssemblyInfo + Assembly Assembly information. Examples -------- @@ -92,7 +92,7 @@ def assembly_info( metadata = get_assembly_metadata(cls, assembly=assembly) - return AssemblyInfo( + return Assembly( assembly=assembly, species=metadata["species"], common_name=metadata["common_name"], diff --git a/genomeinfo/core/chrom.py b/assemblyinfo/core/chrom.py similarity index 95% rename from genomeinfo/core/chrom.py rename to assemblyinfo/core/chrom.py index 6da8c68..6f74631 100644 --- a/genomeinfo/core/chrom.py +++ b/assemblyinfo/core/chrom.py @@ -44,7 +44,7 @@ def filter_chromosome_data( Examples -------- - >>> GenomeInfo.filter_chromosome_data("hg38", roles=["assembled"]) + >>> AssemblyInfo.filter_chromosome_data("hg38", roles=["assembled"]) """ if assembly in cls._data["assembly"].tolist(): group = "assembly" @@ -121,7 +121,7 @@ def get_chromnames( Examples -------- - >>> GenomeInfo.get_chromnames("hg38", provider="ucsc") + >>> AssemblyInfo.get_chromnames("hg38", provider="ucsc") """ if not provider or provider == "ucsc": colname = "name" @@ -173,7 +173,7 @@ def get_chromsizes( Examples -------- - >>> GenomeInfo.get_chromsizes("hg38", provider="ucsc") + >>> AssemblyInfo.get_chromsizes("hg38", provider="ucsc") """ if not provider or provider == "ucsc": colname = "name" @@ -226,7 +226,7 @@ def get_chrom_eq( Examples -------- - >>> GenomeInfo.get_chrom_eq("hg38", providers=["ucsc", "genbank"]) + >>> AssemblyInfo.get_chrom_eq("hg38", providers=["ucsc", "genbank"]) """ if not providers: providers = ["name", "ncbi", "genbank", "refseq"] @@ -257,7 +257,7 @@ def get_seqinfo(cls, assembly: str) -> pd.DataFrame: Examples -------- - >>> GenomeInfo.get_seqinfo("hg38") + >>> AssemblyInfo.get_seqinfo("hg38") """ if assembly in cls._data["assembly"].tolist(): group = "assembly" diff --git a/genomeinfo/core/info.py b/assemblyinfo/core/info.py similarity index 93% rename from genomeinfo/core/info.py rename to assemblyinfo/core/info.py index a9ed725..36643c1 100644 --- a/genomeinfo/core/info.py +++ b/assemblyinfo/core/info.py @@ -21,14 +21,14 @@ def get_db(cls) -> pd.DataFrame: """ - Returns the GenomeInfo database. + Returns the AssemblyInfo database. This method returns the database stored in the class attribute `_data`. Parameters ---------- cls : type - The class object containing the GenomeInfo data. + The class object containing the AssemblyInfo data. Returns ------- @@ -37,7 +37,7 @@ def get_db(cls) -> pd.DataFrame: Examples -------- - >>> GenomeInfo.get_db() + >>> AssemblyInfo.get_db() """ return cls._data @@ -45,16 +45,16 @@ def get_db(cls) -> pd.DataFrame: def info(cls) -> str: """ - Display information about available entries in GenomeInfo. + Display information about available entries in AssemblyInfo. This method prints a formatted message showing the unique values for species, UCSC assemblies, and NCBI assemblies available in the - GenomeInfo data. + AssemblyInfo data. Parameters ---------- cls : type - The class object containing the GenomeInfo data. + The class object containing the AssemblyInfo data. Returns ------- @@ -63,9 +63,9 @@ def info(cls) -> str: Examples -------- - >>> GenomeInfo.info() + >>> AssemblyInfo.info() ``` - GenomeInfo available entries: + AssemblyInfo available entries: Species: human, mouse, rat Assemblies (UCSC): @@ -123,7 +123,7 @@ def get_info(cls, key: str, value: Optional[str]) -> pd.DataFrame: Examples -------- - >>> GenomeInfo.get_info("species", "homo_sapiens") + >>> AssemblyInfo.get_info("species", "homo_sapiens") """ if value is None: raise ValueError(f"ERROR! Pick a {key}: {cls._data[key].unique()}") @@ -163,7 +163,7 @@ def get_species_info(cls, species: Optional[str] = None) -> str: Examples -------- - >>> GenomeInfo.get_species_info("species", "homo_sapiens") + >>> AssemblyInfo.get_species_info("species", "homo_sapiens") ``` Genome Information for homo_sapiens: Common Names: @@ -201,7 +201,7 @@ def get_organism_info(cls, organism: Optional[str] = None) -> str: Examples -------- - >>> GenomeInfo.get_species_info("species", "homo_sapiens") + >>> AssemblyInfo.get_species_info("species", "homo_sapiens") ``` Genome Information for human: Species: @@ -249,7 +249,7 @@ def get_assembly_metadata(cls, assembly: Optional[str] = None) -> Dict[str, Any] Examples -------- - >>> GenomeInfo.get_assembly_metadata("hg38") + >>> AssemblyInfo.get_assembly_metadata("hg38") { 'assembly_level': 'Chromosome', 'assembly_method': None, @@ -316,7 +316,7 @@ def build_assembly_info(cls, local_db: pd.DataFrame, assembly: str) -> Dict[str, Examples -------- - >>> GenomeInfo.build_assembly_info(local_db, "hg38") + >>> AssemblyInfo.build_assembly_info(local_db, "hg38") """ if len(local_db.patch) > 1: latest = sorted(local_db.patch.tolist(), key=get_version, reverse=True)[0] @@ -357,7 +357,7 @@ def available_assemblies(cls, provider: Optional[str] = None) -> List[str]: Examples -------- - >>> GenomeInfo.available_assemblies() + >>> AssemblyInfo.available_assemblies() ``` ['WS144', 'WBcel215', @@ -397,7 +397,7 @@ def available_patches(cls, assembly: Optional[str] = None) -> List[str]: Examples -------- - >>> GenomeInfo.available_patches('GRCh38') + >>> AssemblyInfo.available_patches('GRCh38') ``` ['GRCh38', 'GRCh38.p1', @@ -433,7 +433,7 @@ def available_species(cls) -> List[str]: Examples -------- - >>> GenomeInfo.available_species() + >>> AssemblyInfo.available_species() ``` ['homo_sapiens', 'mus_musculus'] ``` @@ -462,7 +462,7 @@ def available_accessions(cls, assembly: str) -> List[str]: Examples --------- - >>> GenomeInfo.available_accessions('hg38') + >>> AssemblyInfo.available_accessions('hg38') ``` ['GCA_000001405.15', 'GCA_000001405.16', diff --git a/genomeinfo/data/db.parquet b/assemblyinfo/data/db.parquet similarity index 100% rename from genomeinfo/data/db.parquet rename to assemblyinfo/data/db.parquet diff --git a/genomeinfo/data/init_db.tsv b/assemblyinfo/data/init_db.tsv similarity index 100% rename from genomeinfo/data/init_db.tsv rename to assemblyinfo/data/init_db.tsv diff --git a/genomeinfo/interface.py b/assemblyinfo/interface.py similarity index 84% rename from genomeinfo/interface.py rename to assemblyinfo/interface.py index 28b60c8..e005c20 100644 --- a/genomeinfo/interface.py +++ b/assemblyinfo/interface.py @@ -4,10 +4,10 @@ import pyarrow.parquet as pq -__all__ = ["GenomeInfo"] +__all__ = ["AssemblyInfo"] -class GenomeInfo: +class AssemblyInfo: _instance = None _db_path = Path(__file__).parent / "data" / "db.parquet" @@ -23,5 +23,5 @@ def _load_db(self) -> None: @classmethod def connect(cls): - """Returns the singleton instance of GenomeInfo.""" + """Returns the singleton instance of AssemblyInfo.""" return cls() diff --git a/docs/conf.py b/docs/conf.py index b23036c..d63debc 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -9,9 +9,9 @@ # -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -info = metadata("genomeinfo") +info = metadata("assemblyinfo") project_name = info["Name"] -project = "GenomeInfo" +project = "AssemblyInfo" author = "Open2C" copyright = f"{datetime.now():%Y}, {author}." version = info["Version"] diff --git a/docs/index.rst b/docs/index.rst index 6e78119..af0df6c 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,12 +1,12 @@ -.. GenomeInfo documentation master file, created by +.. assemblyinfo documentation master file, created by sphinx-quickstart on Sat Jul 6 23:33:22 2024. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -genomeinfo -========== +assemblyinfo +============ -`Genomeinfo `_ is a library to interact with genome metadata from different providers in python. This package is build on top of NCBI and UCSC data, allowing fast and accurate interconversions between chromosome names, latest assemblies and more! +`Assemblyinfo `_ is a library to interact with genome metadata from different providers in python. This package is build on top of NCBI and UCSC data, allowing fast and accurate interconversions between chromosome names, latest assemblies and more! .. toctree:: :maxdepth: 2 diff --git a/docs/quickstart.md b/docs/quickstart.md index ff63dd5..af4566d 100644 --- a/docs/quickstart.md +++ b/docs/quickstart.md @@ -3,18 +3,18 @@ ## Installation ``` -$ pip install genomeinfo +$ pip install assemblyinfo ``` To install the latest development version of bioframe from github, first make a local clone of the github repository: ``` -$ git clone https://github.com/open2c/genomeinfo +$ git clone https://github.com/open2c/assemblyinfo ``` Then, compile and install bioframe in [development mode](https://setuptools.readthedocs.io/en/latest/setuptools.html#development-mode). This installs the package without moving it to a system folder, and thus allows for testing changes to the python code on the fly. ``` -$ cd bioframe +$ cd assemblyinfo $ pip install -e ./ ``` diff --git a/pyproject.toml b/pyproject.toml index 1e51b18..2884bad 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,8 +3,8 @@ requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" [project] -name = "genomeinfo" -version = "0.1.0" +name = "assemblyinfo" +version = "0.0.1" description = "A Python library for working with harmonized genome metadata" license = {text = "MIT"} authors = [ @@ -55,13 +55,13 @@ docs = [ ] [project.urls] -homepage = "https://github.com/open2c/genomeinfo" -documentation = "https://genomeinfo.readthedocs.io" -repository = "https://github.com/open2c/genomeinfo" -changelog = "https://github.com/open2c/genomeinfo/blob/main/CHANGES.md" +homepage = "https://github.com/open2c/assemblyinfo" +documentation = "https://assemblyinfo.readthedocs.io" +repository = "https://github.com/open2c/assemblyinfo" +changelog = "https://github.com/open2c/assemblyinfo/blob/main/CHANGES.md" [tool.hatch.build.targets.wheel] -packages = ["genomeinfo"] +packages = ["assemblyinfo"] [tool.ruff] target-version = "py37" @@ -83,7 +83,7 @@ extend-select = [ ] [tool.ruff.lint.isort] -known-first-party = ["genomeinfo"] +known-first-party = ["assemblyinfo"] [tool.ruff.lint.pydocstyle] convention = "numpy" @@ -107,8 +107,8 @@ features = ["dev", "docs"] [tool.hatch.envs.default.scripts] fix = "ruff check --fix ." -lint = "ruff check genomeinfo tests" -format = "ruff format genomeinfo tests" +lint = "ruff check assemblyinfo tests" +format = "ruff format assemblyinfo tests" docs = "sphinx-autobuild docs docs/_build/html" [tool.hatch.envs.test] diff --git a/tests/test_core_acc.py b/tests/test_core_acc.py index f7f30cb..00f119e 100644 --- a/tests/test_core_acc.py +++ b/tests/test_core_acc.py @@ -1,10 +1,10 @@ import pytest -from genomeinfo.interface import GenomeInfo +from assemblyinfo.interface import AssemblyInfo def test_get_genbank_accession(): - db = GenomeInfo.connect() + db = AssemblyInfo.connect() result = db.get_genbank_accession("GRCh38.p14") assert result == ["GCA_000001405.29"] @@ -17,7 +17,7 @@ def test_get_genbank_accession(): def test_get_refseq_accession(): - db = GenomeInfo.connect() + db = AssemblyInfo.connect() result = db.get_refseq_accession("GRCh38.p14") assert result == ["GCF_000001405.40"] @@ -30,7 +30,7 @@ def test_get_refseq_accession(): def test_get_patch_from_accession(): - db = GenomeInfo.connect() + db = AssemblyInfo.connect() result = db.get_patch_from_accession("GCF_000001405.40") assert result == ["GRCh38.p14"] @@ -43,7 +43,7 @@ def test_get_patch_from_accession(): def test_get_assembly_from_accession(): - db = GenomeInfo.connect() + db = AssemblyInfo.connect() result = db.get_assembly_from_accession("GCA_000001405.29") assert result == ["GRCh38", "hg38"] diff --git a/tests/test_core_assembly.py b/tests/test_core_assembly.py index 16d5e8e..d630d1f 100644 --- a/tests/test_core_assembly.py +++ b/tests/test_core_assembly.py @@ -1,21 +1,21 @@ -from genomeinfo.core.assembly import AssemblyInfo -from genomeinfo.interface import GenomeInfo +from assemblyinfo.core.assembly import Assembly +from assemblyinfo.interface import AssemblyInfo def test_assembly_info_human(): - db = GenomeInfo.connect() + db = AssemblyInfo.connect() assembly = db.assembly_info(assembly="GRCh38") - assert isinstance(assembly, AssemblyInfo) + assert isinstance(assembly, Assembly) assert assembly.assembly == "GRCh38" assert assembly.species == "homo_sapiens" assert assembly.common_name == "human" assembly = db.assembly_info(assembly="hg38") - assert isinstance(assembly, AssemblyInfo) + assert isinstance(assembly, Assembly) assert assembly.assembly == "hg38" assert assembly.species == "homo_sapiens" assert assembly.common_name == "human" diff --git a/tests/test_core_chrom.py b/tests/test_core_chrom.py index f370fd7..145b85a 100644 --- a/tests/test_core_chrom.py +++ b/tests/test_core_chrom.py @@ -1,11 +1,11 @@ import pandas as pd import pytest -from genomeinfo.interface import GenomeInfo +from assemblyinfo.interface import AssemblyInfo def test_filter_chromosome_data(): - db = GenomeInfo.connect() + db = AssemblyInfo.connect() result = db.filter_chromosome_data("GRCh38", roles=["assembled"]) assert isinstance(result, pd.DataFrame) @@ -35,7 +35,7 @@ def test_filter_chromosome_data(): def test_get_chromnames(): - db = GenomeInfo.connect() + db = AssemblyInfo.connect() result = db.get_chromnames("GRCh38", roles=["assembled"]) assert isinstance(result, list) @@ -50,7 +50,7 @@ def test_get_chromnames(): def test_get_chromsizes(): - db = GenomeInfo.connect() + db = AssemblyInfo.connect() result = db.get_chromsizes("GRCh38", roles=["assembled"]) assert isinstance(result, pd.Series) @@ -65,7 +65,7 @@ def test_get_chromsizes(): def test_get_seqinfo(): - db = GenomeInfo.connect() + db = AssemblyInfo.connect() result = db.get_seqinfo("GRCh38") assert isinstance(result, pd.DataFrame) diff --git a/tests/test_core_info.py b/tests/test_core_info.py index d863507..c5acef5 100644 --- a/tests/test_core_info.py +++ b/tests/test_core_info.py @@ -1,19 +1,19 @@ -from genomeinfo.interface import GenomeInfo +from assemblyinfo.interface import AssemblyInfo def test_method_attachment(): - db = GenomeInfo.connect() + db = AssemblyInfo.connect() assert hasattr(db, "info"), "Method info is not attached" def test_method_execution(): - genome_info = GenomeInfo.connect() + genome_info = AssemblyInfo.connect() genome_info.info() def test_get_species_info(): - genome_info = GenomeInfo.connect() + genome_info = AssemblyInfo.connect() assert hasattr( genome_info, "get_species_info" @@ -26,7 +26,7 @@ def test_get_species_info(): def test_get_assembly_metadata_ncbi(): - genome_info = GenomeInfo.connect() + genome_info = AssemblyInfo.connect() assert hasattr( genome_info, "get_assembly_metadata" @@ -39,7 +39,7 @@ def test_get_assembly_metadata_ncbi(): def test_get_assembly_metadata_ucsc(): - genome_info = GenomeInfo.connect() + genome_info = AssemblyInfo.connect() rs = genome_info.get_assembly_metadata("hg38") @@ -49,7 +49,7 @@ def test_get_assembly_metadata_ucsc(): def test_get_assembly_metadata_t2t(): - genome_info = GenomeInfo.connect() + genome_info = AssemblyInfo.connect() rs = genome_info.get_assembly_metadata("T2T-CHM13") @@ -58,7 +58,7 @@ def test_get_assembly_metadata_t2t(): def test_available_assemblies(): - genome_info = GenomeInfo.connect() + genome_info = AssemblyInfo.connect() rs = genome_info.available_assemblies() @@ -67,7 +67,7 @@ def test_available_assemblies(): def test_get_organism_info(): - genome_info = GenomeInfo.connect() + genome_info = AssemblyInfo.connect() rs = genome_info.get_organism_info("human") @@ -76,7 +76,7 @@ def test_get_organism_info(): def test_available_patches(): - genome_info = GenomeInfo.connect() + genome_info = AssemblyInfo.connect() rs = genome_info.available_patches() @@ -85,7 +85,7 @@ def test_available_patches(): def test_available_accessions(): - genome_info = GenomeInfo.connect() + genome_info = AssemblyInfo.connect() rs = genome_info.available_accessions("GRCh38")