Initial cli

setup.cfg

@@ -50,7 +50,7 @@ ignore =
 [isort]
 default_section = THIRDPARTY
 known_first_party = sgkit
-known_third_party = dask,numpy,pysnptools,pytest,xarray
+known_third_party = dask,numpy,pysnptools,pytest,setuptools,xarray
 multi_line_output = 3
 include_trailing_comma = True
 force_grid_wrap = 0
@@ -62,3 +62,7 @@ ignore_missing_imports = True
 
 [mypy-sgkit_plink.tests.*]
 disallow_untyped_defs = False
+
+[options.entry_points]
+console_scripts =
+    plink2sg = sgkit_plink.cli:plink2sg_main

setup.py

@@ -0,0 +1,4 @@
+#!/usr/bin/env python
+from setuptools import setup
+
+setup(use_scm_version=True)

sgkit_plink/__main__.py

@@ -0,0 +1,4 @@
+from . import cli
+
+if __name__ == "__main__":
+    cli.sgkit_plink_main()

sgkit_plink/cli.py

@@ -0,0 +1,95 @@
+"""
+Command line utilities for conversion.
+"""
+import argparse
+import os
+import signal
+
+from dask.diagnostics import ProgressBar
+
+from . import read_plink
+
+
+def set_sigpipe_handler():
+    if os.name == "posix":
+        # Set signal handler for SIGPIPE to quietly kill the program.
+        signal.signal(signal.SIGPIPE, signal.SIG_DFL)
+
+
+def run_plink2sg(args):
+    # TODO add args for bim and fam seps
+    # TODO add logging and verbosity so we can write out info messages
+    # about what we're doing here.
+    ds = read_plink(args.plink_path, bim_sep=" ", fam_sep=" ")
+
+    # TODO add a command line options for this progess bar.
+    with ProgressBar():
+
+        # TODO Do the dask compute manually so that we can have
+        # more influence over the number of threads used.
+
+        # TODO add options to give more control over the zarr
+        # format used. We probably want to have the option of
+        # writing to a ZipFile anyway, so that we don't have
+        # gazillions of files.
+
+        # TODO catch keyboard interrups here, clean up the
+        # zarr file, and write a meaningful error message.
+        ds.to_zarr(args.sgkit_path, mode="w")
+    # TODO write out an INFO summary of the size of the
+    # input and output
+
+
+def add_plink2sg_arguments(parser):
+
+    # TODO we don't seem to have an __version__ defined yet.
+    # parser.add_argument(
+    #     "-V",
+    #     "--version",
+    #     action="version",
+    #     version=f"%(prog)s {sgkit_plink.__version__}",
+    # )
+
+    parser.add_argument("plink_path", help="The plink dataset to read")
+    parser.add_argument("sgkit_path", help="The path to write the converted dataset to")
+
+
+def get_plink2sg_parser(parser=None):
+
+    parser = argparse.ArgumentParser(description="Convert plink files to sgkit format")
+    add_plink2sg_arguments(parser)
+
+    return parser
+
+
+def get_sgkit_plink_parser():
+    top_parser = argparse.ArgumentParser(
+        description=("Utilities for converting data from plink to sgkit and vice versa")
+    )
+    subparsers = top_parser.add_subparsers(dest="subcommand")
+    subparsers.required = True
+    parser = subparsers.add_parser("plink2sg")
+    parser.set_defaults(runner=run_plink2sg)
+    add_plink2sg_arguments(parser)
+    # TODO add sg2plink also
+    return top_parser
+
+
+def plink2sg_main(arg_list=None):
+    """
+    Top-level hook for the plink2sg console script.
+    """
+    parser = get_plink2sg_parser()
+    args = parser.parse_args(arg_list)
+    args.runner(args)
+
+
+def sgkit_plink_main(arg_list=None):
+    """
+    Top-level hook called when running python -m sgkit_plink. Just
+    exists to call plink2sg or sg2plink as subcommands.
+    """
+    parser = get_sgkit_plink_parser()
+    set_sigpipe_handler()
+    args = parser.parse_args(arg_list)
+    args.runner(args)