genoray-cli 0.1.0__tar.gz

genoray_cli-0.1.0/.gitattributes

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+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

genoray_cli-0.1.0/.gitignore

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genoray_cli-0.1.0/.pre-commit-config.yaml

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+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v6.0.0
+  hooks:
+  - id: check-merge-conflict
+  - id: debug-statements
+  - id: mixed-line-ending
+  - id: check-case-conflict
+  - id: check-yaml
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.13.3
+  hooks:
+  - id: ruff
+  - id: ruff-format
+- repo: https://github.com/commitizen-tools/commitizen
+  rev: v4.9.1
+  hooks:
+  - id: commitizen
+    stages: [commit-msg]
+  - id: commitizen-branch
+    stages: [pre-push]
+    args: [--rev-range=origin/main..]
+
+ci:
+  autofix_commit_msg: |
+        chore(pre-commit): auto fixes from pre-commit.com hooks
+
+        for more information, see https://pre-commit.ci
+  autoupdate_commit_msg: 'chore(pre-commit.ci): pre-commit autoupdate'

genoray_cli-0.1.0/CHANGELOG.md

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+## 0.1.0 (2025-10-09)
+
+### Feat
+
+- commit for bumping

genoray_cli-0.1.0/LICENSE

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+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.

genoray_cli-0.1.0/PKG-INFO

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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/README.md

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+# genoray-cli
+CLI for genoray

genoray_cli-0.1.0/genoray_cli/__main__.py

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+#! /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()