.

Author: vsc20958

.gitignore

@@ -0,0 +1,20 @@
+## Python build artifacts
+__pycache__/
+*.py[cod]
+*.so
+
+## Packaging
+build/
+dist/
+*.egg-info/
+
+## Virtual environments
+.venv/
+venv/
+ENV/
+
+## Tooling caches
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+

README.md

@@ -1,5 +1,7 @@
 # RecMpox
 
+Current release: **v0.0.2**
+
 RecMpox is a command-line tool that **flags potential recombination events** in monkeypox viruses. It does not confirm recombination, but highlights genomes that may be recombinant and warrant further investigation. RecMpox works by detecting regions within a genome that appear to originate from two different parental viruses. Such patterns are not conclusive evidence of recombination, as similar signals can also arise from shared ancestral variation, convergent mutations, mixed populations (e.g., co-infections or laboratory contamination), or sequencing and assembly errors.
 
 
@@ -27,9 +29,10 @@ bash Miniconda3-latest-Linux-x86_64.sh
 
 Then, ensure you have the required channels:
 ```bash
-conda config --add channels defaults
-conda config --add channels bioconda
 conda config --add channels conda-forge
+conda config --add channels bioconda
+conda config --add channels defaults
+conda config --set channel_priority strict
 ```
 
 ### Option 1: Using Conda (Recommended)
@@ -71,15 +74,15 @@ conda activate recmpox
 ```bash
 # Use built-in references: Ia vs Ib or IIa vs IIb (sequences downloaded automatically)
 recmpox -i fasta/ -o output -ref Ia,Ib -t 4
-recmpox -i fasta/ -o output -ref IIa,IIb -t 4
+recmpox -i fasta/ -o output -ref Ib,IIb -t 4
 
 # Input can be: FASTA file, directory of .fa/.fasta/.fna, or NCBI accession(s)
 recmpox -i consensus.fa -o output -ref Ia,Ib
-recmpox -i OZ375330.1,PX739443.1 -o output -ref IIa,IIb
+recmpox -i OZ375330.1 -o output -ref Ib,IIb   # UK recombinant case example
 recmpox -i accessions.txt -o output -ref Ia,Ib   # one accession per line or comma-separated
 ```
 
-**Note**: Either `-ref` (e.g. `Ia,Ib` or `IIa,IIb`) or both `-ref1` and `-ref2` are required. With `-ref`, default references are used (Ia=OZ254474.1, Ib=PP601219.1, IIa=OZ287284.1, IIb=NC_063383.1).
+**Note**: Either `-ref` (e.g. `Ia,Ib`, `IIa,IIb`, or `Ib,IIb`) or both `-ref1` and `-ref2` are required. With `-ref`, default references are used (Ia=OZ254474.1, Ib=PP601219.1, IIa=OZ287284.1, IIb=NC_063383.1).
 
 ### Command-line options
 

conda-recipes/meta.yaml

@@ -14,6 +14,7 @@ build:
   noarch: python
   entry_points:
     - recmpox=recmpox.recmpox:main
+    - rempox=recmpox.recmpox:main
   script:
     - "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
     - mkdir -p $PREFIX/etc/conda/activate.d

recmpox/__init__.py

@@ -1,6 +1,6 @@
 """RecMpox: Classify consensus mpox genomes at diagnostic SNPs (recombinant calling)."""
 
-__version__ = "0.0.2"
+from ._version import __version__
 
 from .recmpox import main
 

recmpox/_version.py

@@ -0,0 +1,2 @@
+__version__ = "0.0.2"
+

recmpox/recmpox.py

@@ -31,6 +31,7 @@
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple
 
+from ._version import __version__
 from .diagnostic_snp import (
     allegiance_summary,
     allegiance_summary_snp_only,
@@ -1198,14 +1199,16 @@ def split_fasta_into_seqs(fasta: Path, out_dir: Path) -> List[Path]:
 
 def main() -> None:
     parser = argparse.ArgumentParser(
-        description="RecMpox: Recombination flagging of mpox sequences (Ia vs Ib).",
+        prog="recmpox",
+        description=f"RecMpox v{__version__}: Flag potential recombination in mpox consensus genomes using diagnostic sites between two reference lineages.",
         formatter_class=argparse.RawDescriptionHelpFormatter,
         add_help=False,
         epilog="""
 Examples:
-  # Use built-in defaults: -ref Ia,Ib (ref1=OZ254474.1, ref2=PP601219.1) or -ref IIa,IIb
+  # Use built-in defaults (Ia=OZ254474.1, Ib=PP601219.1, IIa=OZ287284.1, IIb=NC_063383.1)
   recmpox -i fasta/ -o output -ref Ia,Ib
-  recmpox -i fasta/ -o output -ref IIa,IIb
+  recmpox -i OZ375330.1 -o output -ref Ib,IIb  # UK recombinant case example
+  recmpox -i accessions.txt -o output -ref Ia,Ib
 
   # Override references: -ref1/-ref2 with optional -ref1_g/-ref2_g
   recmpox -i fasta/ -o output -ref1 NC_003310.1 -ref2 PP601219.1 -ref1_g Ia -ref2_g Ib
@@ -1216,8 +1219,9 @@ def main() -> None:
     required = parser.add_argument_group("required arguments (must specify when running)")
     optional = parser.add_argument_group("optional arguments")
     parser.add_argument("-h", "-help", "--help", action="help", help="show this help message and exit")
+    optional.add_argument("--version", action="version", version=f"RecMpox v{__version__}")
     required.add_argument("-i", "-input", dest="input", type=Path, default=None, metavar="", help="FASTA file, directory of .fa/.fasta/.fna, .txt file of accessions (one per line or comma-separated), NCBI accession, or comma-separated accessions (e.g. -i ACC1,ACC2 or -i accessions.txt)")
-    required.add_argument("-ref", dest="ref", type=str, default=None, metavar="", help="Reference pair: comma-separated subclade labels, e.g. Ia,Ib or IIa,IIb. Uses built-in defaults. Either -ref or both -ref1 and -ref2 are required.")
+    required.add_argument("-ref", dest="ref", type=str, default=None, metavar="", help="Reference pair: two comma-separated labels among Ia, Ib, IIa, IIb (e.g. Ia,Ib or Ib,IIb). Uses built-in defaults. Either -ref or both -ref1 and -ref2 are required.")
     required.add_argument("-ref1", type=str, default=None, metavar="", help="First reference: FASTA path or NCBI accession; overrides ref1 when using -ref. Required if -ref is not used.")
     required.add_argument("-ref2", type=str, default=None, metavar="", help="Second reference: FASTA path or NCBI accession; overrides ref2 when using -ref. Required if -ref is not used.")
     optional.add_argument("-o", "-output", dest="output_dir", type=str, default="output", metavar="", help="Output directory (default: output); path is relative to cwd; always removed and recreated at start of each run")
@@ -1227,6 +1231,12 @@ def main() -> None:
     optional.add_argument("-min-indel-size", type=int, default=100, dest="min_indel_size", metavar="", help="Minimum indel length (bp) for diagnostic indels when using -include-indels (default: 100)")
     optional.add_argument("-t", "-threads", dest="threads", type=int, default=1, metavar="", help="Specify number of threads to use (n=1 by default)")
     optional.add_argument("-q", "-quiet", action="store_true", dest="quiet", help="Log to file only")
+
+    # If called with no arguments, show help (same output as --help) instead of erroring.
+    if len(sys.argv) == 1:
+        parser.print_help()
+        return
+
     args = parser.parse_args()
 
     if args.input is None:

setup.py

@@ -16,6 +16,7 @@
     entry_points={
         "console_scripts": [
             "recmpox=recmpox.recmpox:main",
+            "rempox=recmpox.recmpox:main",
         ],
     },
     classifiers=[