Merge pull request #3 from 136s/dev

ver 0.2.0

ncbi_counts/__version__.py

@@ -1,4 +1,4 @@
 #!/usr/bin/env python
 
-VERSION = (0, 1, 0)
+VERSION = (0, 2, 0)
 __version__ = ".".join(map(str, VERSION))

ncbi_counts/core.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 
+from __future__ import annotations
 from dataclasses import dataclass, field
 from pathlib import Path
 import warnings

ncbi_counts/load.py

@@ -70,12 +70,12 @@ def load_input(input_path: StrPath) -> GeoRegex:
     Returns:
         GeoRegex: Dictionary of regular expressions.
     """
-    match Path(input_path).suffix:
-        case ".yaml" | ".yml":
-            return load_yaml(input_path)
-        case ".csv":
-            return load_csv(input_path)
-        case ".tsv":
-            return load_csv(input_path, sep="\t")
-        case _:
-            raise ValueError("Supported file types are .yaml, .yml, .csv, .tsv.")
+    suf = Path(input_path).suffix
+    if suf in (".yaml" | ".yml"):
+        return load_yaml(input_path)
+    elif suf == ".csv":
+        return load_csv(input_path)
+    elif suf == ".tsv":
+        return load_csv(input_path, sep="\t")
+    else:
+        raise ValueError("Supported file types are .yaml, .yml, .csv, .tsv.")

ncbi_counts/types.py

@@ -1,13 +1,13 @@
 #!/usr/bin/env python
 
 from pathlib import Path
-from typing import Literal
+from typing import Literal, Union
 
 
-StrPath = str | Path
+StrPath = Union[str, Path]
 GseAcc = str
 GsmAcc = str
-Groups = Literal["treatment", "control"] | str
+Groups = Union[Literal["treatment", "control"], str]
 PairRegex = dict[Groups, dict[str, str]]
 GeoRegex = dict[GseAcc, list[PairRegex]]
 PairGsms = dict[Groups, list[GsmAcc]]

ncbi_counts/utils.py

@@ -90,13 +90,12 @@ def get_count_url(
     Returns:
         str: URL of NCBI-generated count file.
     """
-    match norm_type:
-        case None:
-            count_type = "raw_counts"
-        case "fpkm" | "tpm":
-            count_type = "norm_counts_" + norm_type.upper()
-        case _:
-            raise ValueError("Supported normalization types are 'fpkm' and 'tpm'.")
+    if norm_type is None:
+        count_type = "raw_counts"
+    elif norm_type in ("fpkm", "tpm"):
+        count_type = "norm_counts_" + norm_type.upper()
+    else:
+        raise ValueError("Supported normalization types are 'fpkm' and 'tpm'.")
     return (
         GEO_DOWNLOAD_BASE
         + f"type=rnaseq_counts&acc={gse_acc}&format=file&file={gse_acc}_{count_type}_{annot_ver}_NCBI.tsv.gz"

setup.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-
 from pathlib import Path
 from setuptools import setup, find_packages
 
@@ -37,7 +36,7 @@ def readme():
     ],
     url="https://github.com/136s/ncbi_counts",
     packages=find_packages(exclude=("tests", "docs")),
-    python_requires=">=3.10.0",
+    python_requires=">=3.9.0",
     install_requires=["GEOparse", "pandas", "PyYAML"],
     extras_require={"dev": ["pytest", "build", "twine"]},
     keywords=["GEO", "Gene Expression Omnibus", "Bioinformatics", "RNA-seq", "NCBI"],