Merge pull request #7 from not-a-feature/dev

add cli stand-alone version

README.md

@@ -35,6 +35,12 @@ Using pip  / pip3:
 ```bash
 pip install tajimas_d
 ```
+
+Using conda:
+```bash
+conda install -c bioconda tajimas_d
+```
+
 Or by source:
 ```bash
 git clone [email protected]:not-a-feature/tajimas_d.git
@@ -56,13 +62,10 @@ theta_w = watterson_estimator(sequences)
 
 
 ## Standalone version
-
-Clone the repository and cd into it. Intall the requirements (miniFasta >= 2.2, for fasta reading).
-
 ```
-usage: tajimas-d.py [-h] -f PATH [-p] [-t] [-w]
+usage: tajimas_d [-h] -f PATH [-p] [-t] [-w]
 
-tajimas-d: Compute Tajima's D, the Pi- or Watterson-Estimator for multiple
+tajimas_d: Compute Tajima's D, the Pi- or Watterson-Estimator for multiple
 sequences.
 
 optional arguments:

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = tajimas_d
-version = 1.0.5
+version = 2.0.0
 description = Computes Tajimas D, the Pi- or Watterson-Estimator for multiple sequences.
 long_description = file: README.md
 long_description_content_type=text/markdown
@@ -31,8 +31,13 @@ testing =
     tox>=3.20
     miniFasta>=2.2
 
+[options.entry_points]
+console_scripts =
+    tajimas_d = tajimas_d._tajimas_d:run_cli
+
+
 [options.package_data]
-frameshift_aware_alignment = py.typed
+tajimas_d = py.typed
 
 [pytest]
 xfail_strict=true

src/tajimas_d/__init__.py

@@ -1,3 +1,4 @@
-from ._tajimas_d import pi_estimator, watterson_estimator, tajimas_d
+"""Init of the tajimas_d package."""
+from ._tajimas_d import pi_estimator, watterson_estimator, tajimas_d, _main_cli
 
-__all__ = ["pi_estimator", "watterson_estimator", "tajimas_d"]
+__all__ = ["pi_estimator", "watterson_estimator", "tajimas_d", "_main_cli"]

src/tajimas_d/_tajimas_d.py

@@ -9,6 +9,9 @@
 
 from itertools import combinations
 from typing import List
+import argparse
+import miniFasta
+from sys import argv
 
 
 def __check(sequences: List[str]) -> None:
@@ -144,3 +147,95 @@ def tajimas_d(sequences: List[str]) -> float:
     delta_Theta = theta_pi - (seg_sites / harmonic)
     tD = delta_Theta / (((e1 * seg_sites) + (e2 * seg_sites * (seg_sites - 1))) ** 0.5)  # Ref 27
     return float(tD)
+
+
+def parse_args(args):
+    """Parse command line parameters.
+
+    Args:
+      args (List[str]): command line parameters as list of strings
+          (for example  ``["--help"]``).
+
+    Returns:
+      :obj:`argparse.Namespace`: command line parameters namespace
+    """
+    # Parse arguments
+    parser = argparse.ArgumentParser(
+        description="""tajimas_d: Compute Tajima's D, the Pi- or Watterson-Estimator for multiple sequences."""
+    )
+
+    parser.add_argument(
+        "-f",
+        "--file",
+        action="store",
+        dest="path",
+        help="Path to fasta file with all sequences.",
+        required=True,
+    )
+
+    parser.add_argument(
+        "-p",
+        "--pi",
+        action="store_true",
+        dest="pi",
+        help="Compute the Pi-Estimator score. (default)",
+        required=False,
+    )
+
+    parser.add_argument(
+        "-t",
+        "--tajima",
+        action="store_true",
+        dest="tajima",
+        help="Compute Tajima's D",
+        required=False,
+    )
+
+    parser.add_argument(
+        "-w",
+        "--watterson",
+        action="store_true",
+        dest="watterson",
+        help="Compute the Watterson-Estimator score.",
+        required=False,
+    )
+
+    return parser.parse_args()
+
+
+def _main_cli(args):
+    args = parse_args(args)
+    # Load sequences
+    sequences = [mf.body for mf in miniFasta.read(args.path)]
+
+    # Compute
+    if args.tajima or not (args.pi or args.watterson):
+        print(f"Tajima's D score:\t\t{tajimas_d(sequences)}")
+
+    if args.pi:
+        print(f"Pi-Estimator score:\t\t{pi_estimator(sequences)}")
+
+    if args.watterson:
+        print(f"Watterson-Estimator score:\t{watterson_estimator(sequences)}")
+
+
+def run_cli():
+    """Calls :func:`_main_cli` passing the CLI arguments extracted from :obj:`sys.argv`.
+
+    This function is used as entry point to create a console script with setuptools.
+    """
+    _main_cli(argv[1:])
+
+
+if __name__ == "__main__":
+    # ^  This is a guard statement that will prevent the following code from
+    #    being executed in the case someone imports this file instead of
+    #    executing it as a script.
+    #    https://docs.python.org/3/library/__main__.html
+
+    # After installing your project with pip, users can also run your Python
+    # modules as scripts via the ``-m`` flag, as defined in PEP 338::
+    #
+    #     python -m tajimas_d.tajimas_d [ARGS]
+    #
+    run_cli()