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Module Biocaml_bpmap (.ml)

Affymetrix's BPMAP files. Only text format supported. Binary BPMAP files must first be converted to text using Affymetrix's probe exporter tool.

module Biocaml_bpmap:
sig
type probe = {
   org_name : string; (*name of organism on which probe is based*)
   version : string; (*genome build version on which probe is based*)
   chr_name : string; (*name of chromosome on which probe is based*)
   start_pos : int; (*start position of probe on given chromosome*)
   sequence : Biocaml_seq.t; (*sequence of the perfect match probe*)
} 
type row = {
   pmcoord : int * int; (*x,y-coordinates of perfect match probe.*)
   mmcoord : int * int; (*x,y-coordinates of mis-match probe*)
   probe : probe;
}
Type of information on one data row.
type t
Type of a BPMAP file.
exception Bad of string
Raised when encountering ill-formed BPMAP.
val num_probes : t -> int
Number of PM/MM probe pairs in given BPMAP. The number of total probes is twice this value.
val col_names : string list
Names of columns in BPMAP file, in the order required by specification.
val iter : (row -> unit) -> t -> unit
val fold : ('a -> row -> 'a) -> 'a -> t -> 'a
val to_list : t -> row list

I/O

val of_file : ?chr_map:(string -> string) -> string -> t
of_file file parses file. If given, chr_map is applied to every chromosome name. Raise Bad if there is a parse error.
val row_to_string : row -> string
String representation of row in same format as required by specification.
val to_file : string -> t -> unit
to_file file t prints t to file in format required by specification.
end