API: normalization¶
-
blockify.normalization.
normalize
(input_file, regions_bed, libraryFactor, lengthFactor)[source]¶ Core normalization method
- Parameters
input_file (BedTool object) – BedTool object (instantiated from pybedtools) for input data
regions_bed (BedTool object) – BedTool object (instantiated from pybedtools) for regions over which we are normalizing input_file
libraryFactor (float) – Scalar to normalize by input_file’s library size.
lengthFactor (float or None) – Scalar to normalize by each block’s length. If None, no length normalization is performed.
- Returns
bedgraph – A BedTool object in bedGraph format, using the intervals supplied in regions_bed
- Return type
BedTool
-
blockify.normalization.
normalize_from_command_line
(args)[source]¶ Wrapper function for the command line function
blockify normalize
- Parameters
args (
argparse.Namespace
object) – Input from command line- Returns
bedgraph – Normalized command line data in bedGraph format
- Return type
BedTool
-
blockify.normalization.
validateNormalizationArguments
(input_file, regions_bed, libraryFactor, lengthFactor)[source]¶ Validates parameters passed via the command line.
- Parameters
input_file (BedTool object) – BedTool object (instantiated from pybedtools) for input data
regions_bed (BedTool object) – BedTool object (instantiated from pybedtools) for regions over which we are normalizing input_file
libraryFactor (float) – Scalar to normalize by input_file’s library size.
lengthFactor (float or None) – Scalar to normalize by each block’s length. If None, no length normalization is performed.
- Returns
None
- Return type
None