The bed utility to generate UCSC bed files

bed.main(args)

If called as a script, this script will take either a ‘base_dir’, the path representing a directory with the calls for every family as described in the README, or a pickle (serialized version of the family information). Either twins or parents can also be provided, depending on which bed files the user wants to generate.

bed.write_beds(cnvs, output_dir, family_id, twins, algo)

Writes the bed files for a list of CNVs.

Parameters:

• cnvs (dict) – A family CNV structure.
• output_dir (str) – Output directory for the bed files.
• family_id (str) – The family id for track identification (e.g. 1443).
• twins (bool) – Boolean indicating if we want to generate the beds for the twins or for the parents.
• algo (str) – The algorithm used to generate the CNV calls (for track identification).