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Add descriptions for the fixed fields #262

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merged 2 commits into from
Jul 1, 2024
Merged

Add descriptions for the fixed fields #262

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5e9de13
Add descriptions for the fixed fields
Will-Tyler Jun 28, 2024
d8474e9
Fix test
Will-Tyler Jun 28, 2024
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13 changes: 13 additions & 0 deletions bio2zarr/vcf2zarr/vcz.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,16 @@ def inspect(path):

DEFAULT_ZARR_COMPRESSOR = numcodecs.Blosc(cname="zstd", clevel=7)

_fixed_field_descriptions = {
"variant_contig": "An identifier from the reference genome or an angle-bracketed ID"
" string pointing to a contig in the assembly file",
"variant_position": "The reference position",
"variant_id": "List of unique identifiers where applicable",
"variant_allele": "List of the reference and alternate alleles",
"variant_quality": "Phred-scaled quality score",
"variant_filter": "Filter status of the variant",
}


@dataclasses.dataclass
class ZarrArraySpec:
Expand All @@ -46,6 +56,9 @@ class ZarrArraySpec:
filters: list

def __post_init__(self):
if self.name in _fixed_field_descriptions:
self.description = self.description or _fixed_field_descriptions[self.name]

# Ensure these are tuples for ease of comparison and consistency
self.shape = tuple(self.shape)
self.chunks = tuple(self.chunks)
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3 changes: 2 additions & 1 deletion tests/test_vcz.py
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Expand Up @@ -295,7 +295,8 @@ def test_variant_contig(self, schema):
"shape": (9,),
"chunks": (10000,),
"dimensions": ("variants",),
"description": "",
"description": "An identifier from the reference genome or an "
"angle-bracketed ID string pointing to a contig in the assembly file",
"vcf_field": None,
"compressor": {
"id": "blosc",
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