Change: v1.0.3 to v1.0.4

- Change default download dir to common cache dir

Author: moshi4

README.md

@@ -152,7 +152,7 @@ functional annotation and classification results are output.
     -h, --help            show this help message and exit
     -i , --infile         Input query protein fasta file
     -o , --outdir         Output directory
-    -d , --download_dir   Download COG & CDD FTP data directory (Default: './cog_download')
+    -d , --download_dir   Download COG & CDD resources directory (Default: '~/.cache/cogclassifier')
     -t , --thread_num     RPS-BLAST num_thread parameter (Default: MaxThread - 1)
     -e , --evalue         RPS-BLAST e-value parameter (Default: 0.01)
     -v, --version         Print version information

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cogclassifier"
-version = "1.0.3"
+version = "1.0.4"
 description = "A tool for classifying prokaryote protein sequences into COG functional category"
 authors = ["moshi"]
 license = "MIT"

src/cogclassifier/cogclassifier.py

@@ -19,7 +19,7 @@
 import pandas as pd
 import requests
 
-__version__ = "1.0.3"
+__version__ = "1.0.4"
 
 
 def main():
@@ -38,7 +38,7 @@ def main():
 def run(
     query_fasta_file: Union[str, Path],
     outdir: Union[str, Path],
-    download_dir: Union[str, Path] = Path("./cog_download"),
+    download_dir: Union[str, Path] = Path.home() / ".cache" / "cogclassifier",
     thread_num: int = 1,
     evalue: float = 1e-2,
 ) -> None:
@@ -56,7 +56,7 @@ def run(
     download_dir = Path(download_dir)
 
     outdir.mkdir(exist_ok=True)
-    download_dir.mkdir(exist_ok=True)
+    os.makedirs(download_dir, exist_ok=True)
 
     print("# Step1: Download COG & CDD FTP data")
     # Setup COG functional category files
@@ -639,12 +639,12 @@ def get_args() -> argparse.Namespace:
         help="Output directory",
         metavar="",
     )
-    default_dl_dir = "./cog_download"
+    default_dl_dir = Path.home() / ".cache" / "cogclassifier"
     parser.add_argument(
         "-d",
         "--download_dir",
         type=Path,
-        help=f"Download COG & CDD FTP data directory (Default: '{default_dl_dir}')",
+        help=f"Download COG & CDD resources directory (Default: '{default_dl_dir}')",
         default=default_dl_dir,
         metavar="",
     )