genoray-cli 0.1.0__py3-none-any.whl

genoray_cli/__main__.py

@@ -0,0 +1,83 @@
+#! /usr/bin/env python
+
+from importlib.metadata import version
+from pathlib import Path
+from typing import Optional, Union
+
+from cyclopts import App
+
+app = App(
+    help_on_error=True,
+    version=f"[magenta]genoray[/magenta] {version('genoray')}\n[cyan]genoray-cli[/cyan] {version('genoray-cli')}",
+    version_format="rich",
+    help="Tools for genoray, including SVAR files.",
+)
+
+
+@app.command
+def index(source: Path):
+    """Create a genoray index for a VCF or PGEN file."""
+    from genoray import PGEN, VCF
+    from genoray._utils import variant_file_type
+
+    file_type = variant_file_type(source)
+    if file_type == "vcf":
+        vcf = VCF(source)
+        vcf._write_gvi_index()
+    elif file_type == "pgen":
+        _ = PGEN(source)
+    else:
+        raise ValueError(f"Unsupported file type: {source}")
+
+
+@app.command
+def write(
+    source: Path,
+    out: Path,
+    max_mem: str = "1g",
+    overwrite: bool = False,
+    dosages: Optional[Union[bool, Path]] = None,
+) -> None:
+    """
+    Convert a VCF or PGEN file to a SVAR file.
+
+    Parameters
+    ----------
+    source : Path
+        Path to the input VCF or PGEN file.
+    out : Path
+        Path to the output SVAR file.
+    max_mem : str, optional
+        Maximum memory to use for conversion e.g. 1g, 250 MB, etc.
+    overwrite : bool, optional
+        Whether to overwrite the output file if it exists.
+    dosages : bool | Path | None, optional
+        Whether to write dosages. If :code:`source` is a PGEN, this must be a path to a PGEN of dosages.
+        If :code:`source` is a VCF, this should be a boolean.
+    """
+    from genoray import PGEN, VCF, SparseVar
+    from genoray._utils import variant_file_type
+
+    file_type = variant_file_type(source)
+    if file_type == "vcf":
+        vcf = VCF(source)
+        SparseVar.from_vcf(out, vcf, max_mem, overwrite, with_dosages=dosages)
+    elif file_type == "pgen":
+        if dosages is False:
+            dosages = None
+            with_dosages = False
+        elif dosages is True:
+            raise ValueError(
+                "Dosages must be provided as a path to a PGEN if source is a PGEN."
+            )
+        else:
+            with_dosages = True
+
+        pgen = PGEN(source, dosage_path=dosages)
+        SparseVar.from_pgen(out, pgen, max_mem, overwrite, with_dosages=with_dosages)
+    else:
+        raise ValueError(f"Unsupported file type: {source}")
+
+
+if __name__ == "__main__":
+    app()

genoray_cli-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: genoray-cli
+Version: 0.1.0
+Summary: Command line interface for genoray
+Author-email: David Laub <dlaub@ucsd.edu>
+License: MIT License
+        
+        Copyright (c) 2025 David Laub
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+License-File: LICENSE
+Requires-Python: <3.13,>=3.9
+Requires-Dist: cyclopts
+Requires-Dist: genoray
+Description-Content-Type: text/markdown
+
+# genoray-cli
+CLI for genoray

genoray_cli-0.1.0.dist-info/RECORD

@@ -0,0 +1,7 @@
+genoray_cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+genoray_cli/__main__.py,sha256=plHNL0CBZkzFDegi2mXXcIVrtHnF0vBPZh5SikeXqlA,2430
+genoray_cli-0.1.0.dist-info/METADATA,sha256=3oUsBcWj4FTbIDWjnpeB3o5FgHtRHINUuTUjha3n42E,1546
+genoray_cli-0.1.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+genoray_cli-0.1.0.dist-info/entry_points.txt,sha256=zEVH4akzYLF810qEzeFM9J9tdcSYXopO_8X8SgCIshw,53
+genoray_cli-0.1.0.dist-info/licenses/LICENSE,sha256=ubiV4_yGkI9lmTqj0wsoakQI38ZaN4qgI_psNvVWpW4,1067
+genoray_cli-0.1.0.dist-info/RECORD,,

genoray_cli-0.1.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.27.0
+Root-Is-Purelib: true
+Tag: py3-none-any

genoray_cli-0.1.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+genoray = genoray_cli.__main__:app

genoray_cli-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 David Laub
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.