Outputs API¶

This module manages the file structure and tracking of Snakemake workflow outputs.

seqnado.outputs.SeqnadoOutputFiles ¶

Bases: BaseModel

Collection of output files generated by SeqNado.

all_files `property` ¶

all_files: List[str]

Return all files in the output collection.

has_consensus_peaks `property` ¶

has_consensus_peaks

Check if consensus peaks are present in the output files.

select_files ¶

select_files(
    suffix: str,
    include: str | None = None,
    exclude: str | None = None,
    must_include_all_patterns: bool = False,
    use_regex: bool = False,
    case_sensitive: bool = False,
) -> List[str]

Filter files by suffix and optional substring.

Parameters:

Name	Type	Description	Default
`suffix`	`str`	The file suffix to filter by (e.g. ".txt" or "csv").	required
`include`	`str`	Substring or regex pattern that must be present in the file path.	`None`
`exclude`	`str`	Substring or regex pattern that must NOT be present in the file path.	`None`
`must_include_all_patterns`	`bool`	If True, all include patterns must match (AND). If False, any match suffices (OR).	`False`
`use_regex`	`bool`	If True, treat include/exclude as regex patterns.	`False`
`case_sensitive`	`bool`	If True, matching is case-sensitive.	`False`

Returns: List[str]: A list of file paths matching the criteria.

Source code in seqnado/outputs/core.py

def select_files(
    self,
    suffix: str,
    include: str | None = None,
    exclude: str | None = None,
    must_include_all_patterns: bool = False,
    use_regex: bool = False,
    case_sensitive: bool = False,
) -> List[str]:
    """Filter files by suffix and optional substring.

    Args:
        suffix (str): The file suffix to filter by (e.g. ".txt" or "csv").
        include (str, optional): Substring or regex pattern that must be present in the file path.
        exclude (str, optional): Substring or regex pattern that must NOT be present in the file path.
        must_include_all_patterns (bool): If True, all include patterns must match (AND). If False, any match suffices (OR).
        use_regex (bool): If True, treat include/exclude as regex patterns.
        case_sensitive (bool): If True, matching is case-sensitive.
    Returns:
        List[str]: A list of file paths matching the criteria.
    """
    fs = FileSelector(self.files)
    return fs.select(
        suffix=suffix,
        includes=include,
        excludes=exclude,
        case_sensitive=case_sensitive,
        use_regex=use_regex,
        includes_all=must_include_all_patterns,
    )

select_bigwig_subtype ¶

select_bigwig_subtype(
    method: PileupMethod = PileupMethod.DEEPTOOLS,
    scale: DataScalingTechnique = DataScalingTechnique.UNSCALED,
    assay: Assay | None = None,
)

Select bigWig files of a specific subtype.

Parameters:

Name	Type	Description	Default
`method`	`PileupMethod`	The pileup method to filter by.	`DEEPTOOLS`
`scale`	`ScaleMethod`	The scale method to filter by.	`UNSCALED`
`assay`	`Assay`	The assay type to filter by. Defaults to None.	`None`

Returns:

Type	Description
	List[str]: A list of bigWig files matching the specified subtype.