pywombat 0.4.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

pywombat/cli.py

@@ -127,7 +127,20 @@ def cli(
             click.echo("Processing with streaming mode...", err=True)
 
         # Build lazy query
-        lazy_df = pl.scan_csv(input_file, separator="\t")
+        # Force certain columns to string type
+        string_columns = [
+            "FID",
+            "sample_id",
+            "father_id",
+            "mother_id",
+            "FatherBarcode",
+            "MotherBarcode",
+            "sample",
+        ]
+        schema_overrides = {col: pl.Utf8 for col in string_columns}
+        lazy_df = pl.scan_csv(
+            input_file, separator="\t", schema_overrides=schema_overrides
+        )
 
         # Apply formatting transformations
         lazy_df = format_bcftools_tsv_lazy(lazy_df, pedigree_df)
@@ -185,7 +198,18 @@ def debug_variant(
         click.echo(f"Debug mode: searching for {chrom}:{pos}", err=True)
 
     # Read and format the data
-    df = pl.read_csv(input_file, separator="\t")
+    # Force certain columns to string type
+    string_columns = [
+        "FID",
+        "sample_id",
+        "father_id",
+        "mother_id",
+        "FatherBarcode",
+        "MotherBarcode",
+        "sample",
+    ]
+    schema_overrides = {col: pl.Utf8 for col in string_columns}
+    df = pl.read_csv(input_file, separator="\t", schema_overrides=schema_overrides)
     formatted_df = format_bcftools_tsv(df, pedigree_df)
 
     # Filter to matching rows
@@ -771,7 +795,18 @@ def read_pedigree(pedigree_path: Path) -> pl.DataFrame:
         DataFrame with columns: sample_id, father_id, mother_id
     """
     # Try reading with header first
-    df = pl.read_csv(pedigree_path, separator="\t")
+    # Force certain columns to string type
+    string_columns = [
+        "FID",
+        "sample_id",
+        "father_id",
+        "mother_id",
+        "FatherBarcode",
+        "MotherBarcode",
+        "sample",
+    ]
+    schema_overrides = {col: pl.Utf8 for col in string_columns}
+    df = pl.read_csv(pedigree_path, separator="\t", schema_overrides=schema_overrides)
 
     # Check if first row has 'FID' in first column (indicates header)
     if df.columns[0] == "FID" or "sample_id" in df.columns:

{pywombat-0.4.0.dist-info → pywombat-0.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pywombat
-Version: 0.4.0
+Version: 0.5.0
 Summary: A CLI tool for processing and filtering bcftools tabulated TSV files with pedigree support
 Project-URL: Homepage, https://github.com/bourgeron-lab/pywombat
 Project-URL: Repository, https://github.com/bourgeron-lab/pywombat

pywombat-0.5.0.dist-info/RECORD

@@ -0,0 +1,6 @@
+pywombat/__init__.py,sha256=iIPN9vJtsIUhl_DiKNnknxCamLinfayodLLFK8y-aJg,54
+pywombat/cli.py,sha256=0nBlwyRu1Q01a0EHcVyIYtKmgezCWA85pQtEXpnuzL4,44535
+pywombat-0.5.0.dist-info/METADATA,sha256=2Py8xwNxZBD18u4r-tJI_mQezMBg4td3ruWOm61MbdA,4982
+pywombat-0.5.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+pywombat-0.5.0.dist-info/entry_points.txt,sha256=Vt7U2ypbiEgCBlEV71ZPk287H5_HKmPBT4iBu6duEcE,44
+pywombat-0.5.0.dist-info/RECORD,,

pywombat-0.4.0.dist-info/RECORD

@@ -1,6 +0,0 @@
-pywombat/__init__.py,sha256=iIPN9vJtsIUhl_DiKNnknxCamLinfayodLLFK8y-aJg,54
-pywombat/cli.py,sha256=dg38E39VpdJhKQt3aGSHwSiLWn1W8JnUkcsy3ZUHD5w,43518
-pywombat-0.4.0.dist-info/METADATA,sha256=ZKPTIp9ud2AIVbcujg4ciq900DX-UkGs5oafa41jxTQ,4982
-pywombat-0.4.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-pywombat-0.4.0.dist-info/entry_points.txt,sha256=Vt7U2ypbiEgCBlEV71ZPk287H5_HKmPBT4iBu6duEcE,44
-pywombat-0.4.0.dist-info/RECORD,,