package biocaml

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The OCaml Bioinformatics Library

Install

Dune Dependency

github.com Readme Edit opam file Versions (5)

Authors

Maintainers

P

philippe.veber@gmail.com

Sources

biocaml-0.11.2.tbz

sha256=fae219e66db06f81f3fd7d9e44717ccf2d6d85701adb12004ab4ae6d3359dd2d

sha512=f6abd60dac2e02777be81ce3b5acdc0db23b3fa06731f5b2d0b32e6ecc9305fe64f407bbd95a3a9488b14d0a7ac7c41c73a7e18c329a8f18febfc8fd50eccbc6

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

Module `Biocaml_unix.Bpmap`Source

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

Sourcetype 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
*)

}

Sourcetype 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.

Sourcetype t

Type of a BPMAP file.

Sourceexception Bad of string

Raised when encountering ill-formed BPMAP.

Sourceval num_probes : t -> int

Number of PM/MM probe pairs in given BPMAP. The number of total probes is twice this value.

Sourceval col_names : string list

Names of columns in BPMAP file, in the order required by specification.

Sourceval iter : (row -> unit) -> t -> unit

Sourceval fold : ('a -> row -> 'a) -> 'a -> t -> 'a

Sourceval to_list : t -> row list

I/O

Sourceval 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.

Sourceval row_to_string : row -> string

String representation of row in same format as required by specification.

Sourceval to_file : string -> t -> unit

to_file file t prints t to file in format required by specification.

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I/O