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Delegated function initialization to superclass via kwargs (partial response to mentor feedback)
1 parent d632f32 commit 617d522

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Lines changed: 3 additions & 37 deletions

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malariagen_data/anoph/phenotypes.py

Lines changed: 3 additions & 37 deletions
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,7 @@ class AnophelesPhenotypeData:
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Inherited by AnophelesDataResource subclasses (e.g., Ag3).
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"""
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# Type annotations for MyPy
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_url: str
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_fs: fsspec.AbstractFileSystem
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sample_metadata: Callable[..., pd.DataFrame]
@@ -21,43 +22,8 @@ class AnophelesPhenotypeData:
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_prep_sample_sets_param: Callable[..., Any]
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haplotypes: Callable[..., Any]
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def __init__(
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self,
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url: str,
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fs: fsspec.AbstractFileSystem,
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sample_metadata: Callable[..., pd.DataFrame],
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sample_sets: list[str],
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snp_calls: Callable[..., Any],
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prep_sample_sets_param: Callable[..., Any],
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haplotypes: Callable[..., Any],
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):
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"""
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Initialize the AnophelesPhenotypeData class.
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Parameters
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----------
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url : str
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Base URL for accessing phenotype data.
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fs : fsspec.AbstractFileSystem
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File system interface for accessing remote data.
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sample_metadata : callable
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Function to retrieve sample metadata.
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sample_sets : list of str
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List of available sample sets.
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snp_calls : callable
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Function to retrieve SNP calls.
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prep_sample_sets_param : callable
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Function to prepare sample sets parameter.
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haplotypes : callable
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Function to retrieve haplotype data.
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"""
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self._url = url
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self._fs = fs
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self.sample_metadata = sample_metadata
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self.sample_sets = sample_sets
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self.snp_calls = snp_calls
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self._prep_sample_sets_param = prep_sample_sets_param
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self.haplotypes = haplotypes
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def __init__(self, **kwargs):
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super().__init__(**kwargs)
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def _load_phenotype_data(
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self,

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