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mecfs_bio.build_system.task.pipes.shifted_log_pipe

Classes:

ShiftedLogPipe

Bases: DataProcessingPipe

Methods:

Attributes:

base instance-attribute 

base: int

cols_to_exclude instance-attribute 

cols_to_exclude: Sequence[str]

pseudocount class-attribute instance-attribute 

pseudocount: float = 1

process 

process(x: LazyFrame) -> narwhals.LazyFrame
Source code in mecfs_bio/build_system/task/pipes/shifted_log_pipe.py 
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def process(self, x: narwhals.LazyFrame) -> narwhals.LazyFrame:
    schema = x.collect_schema()
    for col_name in schema.keys():
        if col_name not in self.cols_to_exclude:
            x = x.with_columns(
                (narwhals.col(col_name) + self.pseudocount)
                .log(base=self.base)
                .alias(col_name)
            )

    return x

ShiftedLogPipeInclude

Bases: DataProcessingPipe

Methods:

Attributes:

base instance-attribute 

base: int

cols_to_include instance-attribute 

cols_to_include: Sequence[str]

pseudocount class-attribute instance-attribute 

pseudocount: float = 1

process 

process(x: LazyFrame) -> narwhals.LazyFrame
Source code in mecfs_bio/build_system/task/pipes/shifted_log_pipe.py 
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def process(self, x: narwhals.LazyFrame) -> narwhals.LazyFrame:
    for col_name in self.cols_to_include:
        x = x.with_columns(
            (narwhals.col(col_name) + self.pseudocount)
            .log(base=self.base)
            .alias(col_name)
        )
    return x