genoray-cli 0.1.1__py3-none-any.whl → 0.2.0__py3-none-any.whl

genoray_cli/__main__.py

@@ -4,6 +4,7 @@ from __future__ import annotations
 
 from importlib.metadata import version
 from pathlib import Path
+from typing import Union
 
 from cyclopts import App
 
@@ -18,7 +19,8 @@ app = App(
 @app.command
 def index(source: Path):
     """Create a genoray index for a VCF or PGEN file."""
-    from genoray import PGEN, VCF
+    from genoray import VCF
+    from genoray._pgen import _write_index
     from genoray._utils import variant_file_type
 
     file_type = variant_file_type(source)
@@ -26,7 +28,16 @@ def index(source: Path):
         vcf = VCF(source)
         vcf._write_gvi_index()
     elif file_type == "pgen":
-        _ = PGEN(source)
+        index = source.with_suffix(".pvar")
+
+        if not index.exists():
+            index = source.with_suffix(".pvar.zst")
+
+        if not index.exists():
+            raise FileNotFoundError("No index file found.")
+
+        index = index.with_suffix(f"{index.suffix}.gvi")
+        _write_index(index)
     else:
         raise ValueError(f"Unsupported file type: {source}")
 
@@ -37,7 +48,8 @@ def write(
     out: Path,
     max_mem: str = "1g",
     overwrite: bool = False,
-    dosages: bool | str | None = None,
+    dosages: Union[str, None] = None,
+    threads: int | None = None,
 ) -> None:
     """
     Convert a VCF or PGEN file to a SVAR file.
@@ -53,8 +65,12 @@ def write(
     overwrite
         Whether to overwrite the output file if it exists.
     dosages
-        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 must be the name of the FORMAT field to use for dosages.
+        Whether to write dosages.
+        If `source` is a PGEN, this must be a path to a PGEN of dosages.
+        If `source` is a VCF, this must be the name of the FORMAT field to use for dosages.
+        If not provided, dosages will not be written.
+    threads
+        Number of threads to use for conversion. Defaults to the number of available CPU cores.
     """
     from genoray import PGEN, VCF, SparseVar
     from genoray._utils import variant_file_type
@@ -66,29 +82,24 @@ def write(
     else:
         with_dosages = True
 
-    if file_type == "vcf":
-        if isinstance(dosages, bool):
-            raise ValueError(
-                "Dosages must be provided as a string for a VCF FORMAT field if the source is a VCF."
-            )
+    if threads is None:
+        threads = -1
 
+    if file_type == "vcf":
         if dosages is not None and Path(dosages).exists():
             raise ValueError(
                 "The `dosages` argument appears to be a path to an existing file, but VCF requires a FORMAT field name."
             )
 
         vcf = VCF(source, dosage_field=dosages)
-        SparseVar.from_vcf(out, vcf, max_mem, overwrite, with_dosages=with_dosages)
+        SparseVar.from_vcf(
+            out, vcf, max_mem, overwrite, with_dosages=with_dosages, n_jobs=threads
+        )
     elif file_type == "pgen":
-        if dosages is False:
-            dosages = None
-        elif dosages is True:
-            raise ValueError(
-                "Dosages must be provided as a path to a PGEN if source is a PGEN."
-            )
-
         pgen = PGEN(source, dosage_path=dosages)
-        SparseVar.from_pgen(out, pgen, max_mem, overwrite, with_dosages=with_dosages)
+        SparseVar.from_pgen(
+            out, pgen, max_mem, overwrite, with_dosages=with_dosages, n_jobs=threads
+        )
     else:
         raise ValueError(f"Unsupported file type: {source}")
 

{genoray_cli-0.1.1.dist-info → genoray_cli-0.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: genoray-cli
-Version: 0.1.1
+Version: 0.2.0
 Summary: Command line interface for genoray
 Author-email: David Laub <dlaub@ucsd.edu>
 License: MIT License
@@ -25,9 +25,9 @@ License: MIT License
         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-Python: <3.14,>=3.10
 Requires-Dist: cyclopts
-Requires-Dist: genoray
+Requires-Dist: genoray>=2.1.0
 Description-Content-Type: text/markdown
 
 # genoray-cli

genoray_cli-0.2.0.dist-info/RECORD

@@ -0,0 +1,7 @@
+genoray_cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+genoray_cli/__main__.py,sha256=uia1uAAAseRKb8maAOrqsjP8Dthd56F3fm5SBGhj5Co,3084
+genoray_cli-0.2.0.dist-info/METADATA,sha256=qhqwuPHZk43NA3oLeKJeYkkalbQ_Ktf-tuqh146utXQ,1554
+genoray_cli-0.2.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+genoray_cli-0.2.0.dist-info/entry_points.txt,sha256=zEVH4akzYLF810qEzeFM9J9tdcSYXopO_8X8SgCIshw,53
+genoray_cli-0.2.0.dist-info/licenses/LICENSE,sha256=ubiV4_yGkI9lmTqj0wsoakQI38ZaN4qgI_psNvVWpW4,1067
+genoray_cli-0.2.0.dist-info/RECORD,,

{genoray_cli-0.1.1.dist-info → genoray_cli-0.2.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any

genoray_cli-0.1.1.dist-info/RECORD

@@ -1,7 +0,0 @@
-genoray_cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-genoray_cli/__main__.py,sha256=kmKfuqiAPVefh8b7D-ZNWIENNQG-x3klIymFxXxTBdo,2830
-genoray_cli-0.1.1.dist-info/METADATA,sha256=5AuOMhu4upgNzQpBH_94LAx7B5iwhCtUjX0yGGPUlN4,1546
-genoray_cli-0.1.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-genoray_cli-0.1.1.dist-info/entry_points.txt,sha256=zEVH4akzYLF810qEzeFM9J9tdcSYXopO_8X8SgCIshw,53
-genoray_cli-0.1.1.dist-info/licenses/LICENSE,sha256=ubiV4_yGkI9lmTqj0wsoakQI38ZaN4qgI_psNvVWpW4,1067
-genoray_cli-0.1.1.dist-info/RECORD,,