ibed format
ibed files are produced by CHiCAGO software for detecting statistically significant interaction events in Capture HiC data. Each row represents a chromosomal interaction. You can check what such a file looks like here. This module offers a representation of this kind of file (essentially a list of records) and some functions to handle this type.
example:
open Biotk
let () =
Ibed.of_file "data/pchic/mouse.ibed"
|> List.filter (fun i -> i.bait.chr = "chr13")
|> Ibed.to_file "data/pchic/mouse_chr13.ibed" ~header:truetype t = item listSort contacts by the genomic locaction of bait part, ascending by default.
Produce a list of contacts list, each sublist contains all contact that share the same bait.
Produce a list of tuple, first element of the couple is the chromosome, the second is all contacts that belong to this chromosome.
val of_file_exn : string -> tval to_file : t -> path:string -> header:bool -> unit