Load module

fanc.tools.load.load(file_name, *args, **kwargs)

Load a file into your current Python session.

load() is a magic function that replaces the need for importing files using different classes or functions. It “just works” for all objects generated by FAN-C (Hic, ReadPairs, ABCompartmentMatrix, …), for compatible Hi-C files from Cooler or Juicer, and most of the major file formats for genomic regions (BED, GFF, BigWig, Tabix, …).

Simply run

o = fanc.load("/path/to/file")

Depending on the file type, the returned object can be the instance of one (or more) of these classes:

  • RegionBased for genomic region formats (BED, GFF, …, but also most FAN-C objects)

  • RegionMatrixContainer or RegionPairsContainer for read pair or matrix-based FAN-C objects, as well as Cooler and Juicer files

  • AlignmentFile for SAM/BAM files

Parameters

  • file_name – Path to file

  • args – Positional arguments passed to the class/function that can load the file

  • kwargs – Keyword arguments passed to the class/function that can load the file

Returns

object (RegionBased, RegionMatrixContainer, RegionPairsContainer, or AlignmentFile)