genoray-cli 0.1.0__py3-none-any.whl → 0.1.2__py3-none-any.whl

genoray_cli/__main__.py

@@ -1,8 +1,10 @@
 #! /usr/bin/env python
 
+from __future__ import annotations
+
 from importlib.metadata import version
 from pathlib import Path
-from typing import Optional, Union
+from typing import Union
 
 from cyclopts import App
 
@@ -36,43 +38,46 @@ def write(
     out: Path,
     max_mem: str = "1g",
     overwrite: bool = False,
-    dosages: Optional[Union[bool, Path]] = None,
+    dosages: Union[str, None] = None,
 ) -> None:
     """
     Convert a VCF or PGEN file to a SVAR file.
 
     Parameters
     ----------
-    source : Path
+    source
         Path to the input VCF or PGEN file.
-    out : Path
+    out
         Path to the output SVAR file.
-    max_mem : str, optional
+    max_mem
         Maximum memory to use for conversion e.g. 1g, 250 MB, etc.
-    overwrite : bool, optional
+    overwrite
         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.
+    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.
     """
     from genoray import PGEN, VCF, SparseVar
     from genoray._utils import variant_file_type
 
     file_type = variant_file_type(source)
+
+    if dosages is None:
+        with_dosages = False
+    else:
+        with_dosages = True
+
     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:
+        if dosages is not None and Path(dosages).exists():
             raise ValueError(
-                "Dosages must be provided as a path to a PGEN if source is a PGEN."
+                "The `dosages` argument appears to be a path to an existing file, but VCF requires a FORMAT field name."
             )
-        else:
-            with_dosages = True
 
+        vcf = VCF(source, dosage_field=dosages)
+        SparseVar.from_vcf(out, vcf, max_mem, overwrite, with_dosages=with_dosages)
+    elif file_type == "pgen":
         pgen = PGEN(source, dosage_path=dosages)
         SparseVar.from_pgen(out, pgen, max_mem, overwrite, with_dosages=with_dosages)
     else:

{genoray_cli-0.1.0.dist-info → genoray_cli-0.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: genoray-cli
-Version: 0.1.0
+Version: 0.1.2
 Summary: Command line interface for genoray
 Author-email: David Laub <dlaub@ucsd.edu>
 License: MIT License

genoray_cli-0.1.2.dist-info/RECORD

@@ -0,0 +1,7 @@
+genoray_cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+genoray_cli/__main__.py,sha256=MsRY1SYTk_OIDPwPcToX1nvvno86HnEpFFl9-IqDvok,2504
+genoray_cli-0.1.2.dist-info/METADATA,sha256=KcBMLujL41z47WFzdpmT4w79IUERlgacKTHN-MMQ8vA,1546
+genoray_cli-0.1.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+genoray_cli-0.1.2.dist-info/entry_points.txt,sha256=zEVH4akzYLF810qEzeFM9J9tdcSYXopO_8X8SgCIshw,53
+genoray_cli-0.1.2.dist-info/licenses/LICENSE,sha256=ubiV4_yGkI9lmTqj0wsoakQI38ZaN4qgI_psNvVWpW4,1067
+genoray_cli-0.1.2.dist-info/RECORD,,

genoray_cli-0.1.0.dist-info/RECORD

@@ -1,7 +0,0 @@
-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,,