package biocaml

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The OCaml Bioinformatics Library

Install

Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

Maintainers

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biocaml@googlegroups.com

Sources

v0.10.1.tar.gz

md5=4cf944bcae5d36bf47b67f6bcb2455d7

sha512=0262b5768aefd7c080f664c46c88876fce9a658cc6a87358a77b7112c49ae3042e7ab542e76be5738fbaeda853149b308b48d4897960b5c7ae3b4da71d978bd8

doc/biocaml.unix/Biocaml_unix/Bpmap/index.html

Module `Biocaml_unix.Bpmap`

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

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 : 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 mismatch 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.

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