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* feat: Adding BED support for range operations * chore: Streaming documentatiob update * feat: Adding read_table method * feat: Added sort_bedframe operation * feat: Expand
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1 @@ | ||
| DEFAULT_INTERVAL_COLUMNS = ["chrom", "start", "end"] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,138 @@ | ||
| from typing import Union | ||
|
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| import polars as pl | ||
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| @pl.api.register_lazyframe_namespace("pb") | ||
| class PolarsRangesOperations: | ||
| def __init__(self, ldf: pl.LazyFrame) -> None: | ||
| self._ldf = ldf | ||
|
|
||
| def sort( | ||
| self, cols: Union[tuple[str], None] = ["chrom", "start", "end"] | ||
| ) -> pl.LazyFrame: | ||
| """ | ||
| Sort a bedframe. | ||
| !!! note | ||
| Adapted to Polars API from [bioframe.sort_bedframe](https://github.com/open2c/bioframe/blob/2b685eebef393c2c9e6220dcf550b3630d87518e/bioframe/ops.py#L1698) | ||
| Parameters: | ||
| cols: The names of columns containing the chromosome, start and end of the genomic intervals. | ||
| !!! Example | ||
| ```python | ||
| import polars_bio as pb | ||
| df = pb.read_table("https://www.encodeproject.org/files/ENCFF001XKR/@@download/ENCFF001XKR.bed.gz",schema="bed9") | ||
| df.pb.sort().limit(5).collect() | ||
| ``` | ||
| ```plaintext | ||
| <class 'builtins.PyExpr'> | ||
| shape: (5, 9) | ||
| ┌───────┬─────────┬─────────┬──────┬───┬────────┬────────────┬──────────┬──────────┐ | ||
| │ chrom ┆ start ┆ end ┆ name ┆ … ┆ strand ┆ thickStart ┆ thickEnd ┆ itemRgb │ | ||
| │ --- ┆ --- ┆ --- ┆ --- ┆ ┆ --- ┆ --- ┆ --- ┆ --- │ | ||
| │ str ┆ i64 ┆ i64 ┆ str ┆ ┆ str ┆ str ┆ str ┆ str │ | ||
| ╞═══════╪═════════╪═════════╪══════╪═══╪════════╪════════════╪══════════╪══════════╡ | ||
| │ chr1 ┆ 193500 ┆ 194500 ┆ . ┆ … ┆ + ┆ . ┆ . ┆ 179,45,0 │ | ||
| │ chr1 ┆ 618500 ┆ 619500 ┆ . ┆ … ┆ + ┆ . ┆ . ┆ 179,45,0 │ | ||
| │ chr1 ┆ 974500 ┆ 975500 ┆ . ┆ … ┆ + ┆ . ┆ . ┆ 179,45,0 │ | ||
| │ chr1 ┆ 1301500 ┆ 1302500 ┆ . ┆ … ┆ + ┆ . ┆ . ┆ 179,45,0 │ | ||
| │ chr1 ┆ 1479500 ┆ 1480500 ┆ . ┆ … ┆ + ┆ . ┆ . ┆ 179,45,0 │ | ||
| └───────┴─────────┴─────────┴──────┴───┴────────┴────────────┴──────────┴──────────┘ | ||
| ``` | ||
| """ | ||
| return self._ldf.sort(by=cols) | ||
|
|
||
| def expand( | ||
| self, | ||
| pad: Union[int, None] = None, | ||
| scale: Union[float, None] = None, | ||
| side: str = "both", | ||
| cols: Union[list[str], None] = ["chrom", "start", "end"], | ||
| ) -> pl.LazyFrame: | ||
| """ | ||
| Expand each interval by an amount specified with `pad`. | ||
| !!! Note | ||
| Adapted to Polars API from [bioframe.expand](https://github.com/open2c/bioframe/blob/2b685eebef393c2c9e6220dcf550b3630d87518e/bioframe/ops.py#L150) | ||
| Negative values for pad shrink the interval, up to the midpoint. | ||
| Multiplicative rescaling of intervals enabled with scale. Only one of pad | ||
| or scale can be provided. | ||
| Parameters: | ||
| pad : | ||
| The amount by which the intervals are additively expanded *on each side*. | ||
| Negative values for pad shrink intervals, but not beyond the interval | ||
| midpoint. Either `pad` or `scale` must be supplied. | ||
| scale : | ||
| The factor by which to scale intervals multiplicatively on each side, e.g | ||
| ``scale=2`` doubles each interval, ``scale=0`` returns midpoints, and | ||
| ``scale=1`` returns original intervals. Default False. | ||
| Either `pad` or `scale` must be supplied. | ||
| side : | ||
| Which side to expand, possible values are 'left', 'right' and 'both'. | ||
| Default 'both'. | ||
| cols : | ||
| The names of columns containing the chromosome, start and end of the | ||
| genomic intervals. Default values are 'chrom', 'start', 'end'. | ||
| """ | ||
| df = self._ldf | ||
| ck, sk, ek = ["chrom", "start", "end"] if cols is None else cols | ||
| padsk = "pads" | ||
| midsk = "mids" | ||
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| if scale is not None and pad is not None: | ||
| raise ValueError("only one of pad or scale can be supplied") | ||
| elif scale is not None: | ||
| if scale < 0: | ||
| raise ValueError("multiplicative scale must be >=0") | ||
| df = df.with_columns( | ||
| [(0.5 * (scale - 1) * (pl.col(ek) - pl.col(sk))).alias(padsk)] | ||
| ) | ||
| elif pad is not None: | ||
| if not isinstance(pad, int): | ||
| raise ValueError("additive pad must be integer") | ||
| df = df.with_columns([pl.lit(pad).alias(padsk)]) | ||
| else: | ||
| raise ValueError("either pad or scale must be supplied") | ||
| if side == "both" or side == "left": | ||
| df = df.with_columns([(pl.col(sk) - pl.col(padsk)).alias(sk)]) | ||
| if side == "both" or side == "right": | ||
| df = df.with_columns([(pl.col(ek) + pl.col(padsk)).alias(ek)]) | ||
|
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||
| if pad is not None: | ||
| if pad < 0: | ||
| df = df.with_columns( | ||
| [(pl.col(sk) + 0.5 * (pl.col(ek) - pl.col(sk))).alias(midsk)] | ||
| ) | ||
| df = df.with_columns( | ||
| [ | ||
| pl.min_horizontal(pl.col(sk), pl.col(midsk)) | ||
| .cast(pl.Int64) | ||
| .alias(sk), | ||
| pl.max_horizontal(pl.col(ek), pl.col(midsk)) | ||
| .cast(pl.Int64) | ||
| .alias(ek), | ||
| ] | ||
| ) | ||
| if scale is not None: | ||
| df = df.with_columns( | ||
| [ | ||
| pl.col(sk).round(0).cast(pl.Int64).alias(sk), | ||
| pl.col(ek).round(0).cast(pl.Int64).alias(ek), | ||
| ] | ||
| ) | ||
| schema = df.collect_schema().names() | ||
| if padsk in schema: | ||
| df = df.drop(padsk) | ||
| if midsk in schema: | ||
| df = df.drop(midsk) | ||
| return df |
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