Merge pull request #19 from PopovIILab/dev

Refactor package CLI to native Typer subcommands and update metadata to v1.1.0

Author: ilypopv

README.md

@@ -1,17 +1,24 @@
 #!/usr/bin/env python
-
-import argparse
 import logging
+import sys
 from pathlib import Path
+from typing import Optional
 
 import pandas as pd
+import typer
 
 from krakenparser.utils import ensure_output_dir
 
 _log = logging.getLogger(__name__)
 
+app = typer.Typer(
+    name="csv",
+    add_completion=False,
+    context_settings={"help_option_names": ["-h", "--help"]},
+)
+
 
-def convert_to_csv(input_file, output_file):
+def convert_to_csv(input_file: str, output_file: str) -> None:
     in_path = Path(input_file)
     if not in_path.is_file():
         raise FileNotFoundError(f"Input file not found: {in_path}")
@@ -22,26 +29,42 @@ def convert_to_csv(input_file, output_file):
     _log.info("Data converted and saved as '%s'.", output_file)
 
 
-def main() -> None:
-    logging.basicConfig(level=logging.INFO, format="%(message)s")
-    parser = argparse.ArgumentParser(
-        description="Reads a TXT file, reorganizes the data, and converts it into a CSV file."
-    )
-    parser.add_argument(
+@app.callback(invoke_without_command=True)
+def main(
+    ctx: typer.Context,
+    input_file: Optional[str] = typer.Option(
+        None,
         "-i",
         "--input",
-        required=True,
         help="Path to the input TXT file. This file should contain sample names in columns and microbial taxa in rows.",
-    )
-    parser.add_argument(
+    ),
+    output_file: Optional[str] = typer.Option(
+        None,
         "-o",
         "--output",
-        required=True,
         help="Path to the output CSV file. The script will restructure the data and save it here.",
-    )
-    args = parser.parse_args()
-    convert_to_csv(args.input, args.output)
+    ),
+) -> None:
+    """Reads a TXT file, reorganizes the data, and converts it into a CSV file."""
+    logging.basicConfig(level=logging.INFO, format="%(message)s")
+
+    if input_file is None and output_file is None:
+        print(ctx.get_help())
+        raise typer.Exit()
+
+    if not input_file or not output_file:
+        print(
+            "Error: Missing required options '-i / --input' and '-o / --output'.",
+            file=sys.stderr,
+        )
+        raise typer.Exit(code=1)
+
+    try:
+        convert_to_csv(input_file, output_file)
+    except FileNotFoundError as e:
+        print(f"Error: {e}", file=sys.stderr)
+        raise typer.Exit(code=1)
 
 
 if __name__ == "__main__":
-    main()
+    app()

krakenparser/counts/convert2csv.py

@@ -1,15 +1,24 @@
 #!/usr/bin/env python
 
-import argparse
 import logging
 import os
+import sys
 import tempfile
 from pathlib import Path
+from typing import Optional
+
+import typer
 
 _log = logging.getLogger(__name__)
 
+app = typer.Typer(
+    name="process",
+    add_completion=False,
+    context_settings={"help_option_names": ["-h", "--help"]},
+)
+
 
-def modify_taxa_names(line):
+def modify_taxa_names(line: str) -> str:
     prefixes = ["s__", "g__", "f__", "o__", "c__", "p__"]
     for prefix in prefixes:
         if line.startswith(prefix):
@@ -19,7 +28,7 @@ def modify_taxa_names(line):
     return line
 
 
-def process_files(source_file, destination_file):
+def process_files(source_file: str, destination_file: str) -> None:
     src_path = Path(source_file)
     if not src_path.is_file():
         raise FileNotFoundError(f"Source file not found: {src_path}")
@@ -53,26 +62,42 @@ def process_files(source_file, destination_file):
     _log.info(f"Processed {destination_file} successfully.")
 
 
-def main() -> None:
-    logging.basicConfig(level=logging.INFO, format="%(message)s")
-    parser = argparse.ArgumentParser(
-        description="Reads a source file, processes its first line, modifies taxa names in a destination file, and updates it."
-    )
-    parser.add_argument(
+@app.callback(invoke_without_command=True)
+def main(
+    ctx: typer.Context,
+    input_file: Optional[str] = typer.Option(
+        None,
         "-i",
         "--input",
-        required=True,
         help="Path to the source file. This file's first line will be read and modified.",
-    )
-    parser.add_argument(
+    ),
+    output_file: Optional[str] = typer.Option(
+        None,
         "-o",
         "--output",
-        required=True,
         help="Path to the destination file. This file's contents will be updated with cleaned taxa names.",
-    )
-    args = parser.parse_args()
-    process_files(args.input, args.output)
+    ),
+) -> None:
+    """Reads a source file, processes its first line, modifies taxa names in a destination file, and updates it."""
+    logging.basicConfig(level=logging.INFO, format="%(message)s")
+
+    if input_file is None and output_file is None:
+        print(ctx.get_help())
+        raise typer.Exit()
+
+    if not input_file or not output_file:
+        print(
+            "Error: Missing required options '-i / --input' and '-o / --output'.",
+            file=sys.stderr,
+        )
+        raise typer.Exit(code=1)
+
+    try:
+        process_files(input_file, output_file)
+    except FileNotFoundError as e:
+        print(f"Error: {e}", file=sys.stderr)
+        raise typer.Exit(code=1)
 
 
 if __name__ == "__main__":
-    main()
+    app()

krakenparser/counts/processing_script.py

@@ -4,15 +4,23 @@
 Replaces decombine.sh and decombine_viruses.sh.
 """
 
-import argparse
 import logging
 import re
+import sys
 from pathlib import Path
+from typing import Optional
+
+import typer
 
 from krakenparser.utils import ensure_output_dir
 
 _log = logging.getLogger(__name__)
 
+app = typer.Typer(
+    name="split",
+    add_completion=False,
+    context_settings={"help_option_names": ["-h", "--help"]},
+)
 
 _RANKS = [
     ("species", "s__", []),
@@ -23,20 +31,21 @@
     ("phylum", "p__", ["s__", "g__", "f__", "o__", "c__"]),
 ]
 
-_HUMAN_TAXA = {
-    "species": "s__Homo_sapiens",
-    "genus": "g__Homo",
-    "family": "f__Hominidae",
-    "order": "o__Primates",
-    "class": "c__Mammalia",
-    "phylum": "p__Chordata",
-}
+_HUMAN_MARKERS = frozenset(
+    [
+        "s__Homo_sapiens",
+        "g__Homo",
+        "f__Hominidae",
+        "o__Primates",
+        "c__Mammalia",
+        "p__Chordata",
+    ]
+)
 
 _ACCESSION_RE = re.compile(r"(SRS|SRR|SRX|ERS|ERR|ERX|DRS|DRR|DRX)\d*-")
 
 
 def _strip_path_prefix(line: str) -> str:
-    """'d__X|p__Y|s__Z\t10\t20' → 's__Z\t10\t20'"""
     tab = line.find("\t")
     if tab == -1:
         return line
@@ -46,10 +55,20 @@ def _strip_path_prefix(line: str) -> str:
     return _ACCESSION_RE.sub("", segment + rest)
 
 
+def _human_in_line(line: str) -> bool:
+    tab = line.find("\t")
+    path = line[:tab] if tab != -1 else line
+    segments = set(path.split("|"))
+    return bool(segments & _HUMAN_MARKERS)
+
+
 def split_mpa(
     input_file: str,
     output_dir: str,
     viruses_only: bool = False,
+    bacteria_only: bool = False,
+    fungi_only: bool = False,
+    archaea_only: bool = False,
     keep_human: bool = False,
 ) -> None:
     in_path = Path(input_file)
@@ -58,17 +77,28 @@ def split_mpa(
     out_path = ensure_output_dir(output_dir, is_file=False)
     (out_path / "txt").mkdir(exist_ok=True)
 
-    lines = in_path.read_text().splitlines()
-    data_lines = [ln for ln in lines if not ln.startswith("#") and ln.strip()]
+    all_lines = [
+        ln
+        for ln in in_path.read_text().splitlines()
+        if not ln.startswith("#") and ln.strip()
+    ]
 
+    data_lines = all_lines.copy()
     if viruses_only:
         data_lines = [ln for ln in data_lines if "d__Viruses" in ln]
+    if bacteria_only:
+        data_lines = [ln for ln in data_lines if "d__Bacteria" in ln]
+    if fungi_only:
+        data_lines = [ln for ln in data_lines if "k__Fungi" in ln]
+    if archaea_only:
+        data_lines = [ln for ln in data_lines if "d__Archaea" in ln]
 
-    filter_human = not keep_human and not viruses_only
+    if keep_human:
+        human_lines = [ln for ln in all_lines if _human_in_line(ln)]
+        data_lines = list(dict.fromkeys(data_lines + human_lines))
 
     for rank_name, rank_prefix, exclude_prefixes in _RANKS:
         result = []
-        human_pattern = _HUMAN_TAXA[rank_name]
 
         for line in data_lines:
             if rank_prefix not in line:
@@ -77,7 +107,7 @@ def split_mpa(
                 continue
             if any(ep in line for ep in exclude_prefixes):
                 continue
-            if filter_human and human_pattern in line:
+            if not keep_human and _human_in_line(line):
                 continue
             result.append(_strip_path_prefix(line))
 
@@ -87,33 +117,75 @@ def split_mpa(
     _log.info("MPA file split successfully. Output stored in %s", output_dir)
 
 
-def main() -> None:
-    logging.basicConfig(level=logging.INFO, format="%(message)s")
-    parser = argparse.ArgumentParser(
-        description="Split a combined MPA table into per-rank TXT files."
-    )
-    parser.add_argument("-i", "--input", required=True, help="Input combined MPA file")
-    parser.add_argument("-o", "--output", required=True, help="Output directory")
-    parser.add_argument(
-        "--viruses-only",
-        action="store_true",
-        default=False,
-        help="Extract only Viruses domain taxa",
-    )
-    parser.add_argument(
+@app.callback(invoke_without_command=True)
+def main(
+    ctx: typer.Context,
+    input_file: Optional[str] = typer.Option(
+        None,
+        "-i",
+        "--input",
+        help="Input combined MPA file.",
+    ),
+    output_dir: Optional[str] = typer.Option(
+        None,
+        "-o",
+        "--output",
+        help="Output directory.",
+    ),
+    viruses_only: bool = typer.Option(
+        False,
+        "--viruses",
+        help="Extract only VIRUSES domain taxa.",
+    ),
+    bacteria_only: bool = typer.Option(
+        False,
+        "--bacteria",
+        help="Extract only BACTERIA domain taxa.",
+    ),
+    fungi_only: bool = typer.Option(
+        False,
+        "--fungi",
+        help="Extract only FUNGI kingdom taxa.",
+    ),
+    archaea_only: bool = typer.Option(
+        False,
+        "--archaea",
+        help="Extract only ARCHAEA domain taxa.",
+    ),
+    keep_human: bool = typer.Option(
+        False,
         "--keep-human",
-        action="store_true",
-        default=False,
-        help="Do not filter human-related taxa (default: filtered)",
-    )
-    args = parser.parse_args()
-    split_mpa(
-        args.input,
-        args.output,
-        viruses_only=args.viruses_only,
-        keep_human=args.keep_human,
-    )
+        help="Retain human-related taxa (default: filtered out).",
+    ),
+) -> None:
+    """Split a combined MPA table into per-rank TXT files."""
+    logging.basicConfig(level=logging.INFO, format="%(message)s")
+
+    if input_file is None and output_dir is None:
+        print(ctx.get_help())
+        raise typer.Exit()
+
+    if not input_file or not output_dir:
+        print(
+            "Error: Missing required options '-i / --input' and '-o / --output'.",
+            file=sys.stderr,
+        )
+        raise typer.Exit(code=1)
+
+    try:
+        split_mpa(
+            input_file,
+            output_dir,
+            viruses_only=viruses_only,
+            bacteria_only=bacteria_only,
+            fungi_only=fungi_only,
+            archaea_only=archaea_only,
+            keep_human=keep_human,
+        )
+    except FileNotFoundError as e:
+        print(f"Error: {e}", file=sys.stderr)
+        raise typer.Exit(code=1)
 
 
 if __name__ == "__main__":
-    main()
+    app()