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sanghoonioclaude
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Fix ruff formatting in aggregation.py
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
1 parent 3543057 commit d57b578

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Lines changed: 5 additions & 15 deletions

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bbconf/modules/aggregation.py

Lines changed: 5 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -80,9 +80,7 @@ def aggregate_collection(
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# ---------------------------------------------------------------------------
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def _sql_aggregate_composition(
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session: Session, bed_ids: List[str]
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) -> Optional[dict]:
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def _sql_aggregate_composition(session: Session, bed_ids: List[str]) -> Optional[dict]:
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"""Count distinct values per metadata column via SQL GROUP BY."""
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fields = ["genome_alias", "assay", "cell_type", "tissue", "target"]
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result = {}
@@ -116,9 +114,7 @@ def _sql_aggregate_composition(
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return result if result else None
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def _sql_aggregate_scalars(
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session: Session, bed_ids: List[str]
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) -> Optional[dict]:
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def _sql_aggregate_scalars(session: Session, bed_ids: List[str]) -> Optional[dict]:
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"""Compute mean, sd, and histogram for scalar columns in SQL.
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Uses a single query for mean/sd/min/max/count, then width_bucket
@@ -155,9 +151,7 @@ def _sql_aggregate_scalars(
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col_max = float(getattr(row, f"{col}_max"))
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# 2. Histogram via width_bucket (PostgreSQL)
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histogram = _sql_histogram(
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session, bed_ids, col, col_min, col_max, n
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)
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histogram = _sql_histogram(session, bed_ids, col, col_min, col_max, n)
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result[col] = {
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"mean": mean_val,
@@ -349,9 +343,7 @@ def _sql_aggregate_tss_histogram(
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return result
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def _sql_aggregate_partitions(
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session: Session, bed_ids: List[str]
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) -> Optional[dict]:
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def _sql_aggregate_partitions(session: Session, bed_ids: List[str]) -> Optional[dict]:
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"""Aggregate genomic partitions from flat percentage columns.
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Uses the pre-computed *_percentage columns on bed_stats, which are
@@ -373,9 +365,7 @@ def _sql_aggregate_partitions(
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f"COUNT({col}) AS {name}_n"
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for name, col in partition_columns
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)
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sql = text(
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f"SELECT {agg_exprs} FROM bed_stats WHERE id = ANY(:bed_ids)"
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)
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sql = text(f"SELECT {agg_exprs} FROM bed_stats WHERE id = ANY(:bed_ids)")
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row = session.execute(sql, {"bed_ids": bed_ids}).one()
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