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Some logging for plink
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bio2zarr/plink.py

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@@ -90,6 +90,7 @@ def convert(
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chunks=(chunk_width,),
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)
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a.attrs["_ARRAY_DIMENSIONS"] = ["samples"]
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logger.debug(f"Encoded samples")
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# TODO encode these in slices - but read them in one go to avoid
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# fetching repeatedly from bim file
@@ -101,6 +102,7 @@ def convert(
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chunks=(chunk_length,),
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)
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a.attrs["_ARRAY_DIMENSIONS"] = ["variants"]
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logger.debug(f"encoded variant_position")
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alleles = np.stack([bed.allele_1, bed.allele_2], axis=1)
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a = root.array(
@@ -111,6 +113,7 @@ def convert(
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chunks=(chunk_length,),
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)
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a.attrs["_ARRAY_DIMENSIONS"] = ["variants", "alleles"]
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logger.debug(f"encoded variant_allele")
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# TODO remove this?
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a = root.empty(

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