Module Biocaml_genomeMap (.ml)

Data structures to represent sets of (possibly annotated) genomic regions

This module is useful to deal with sets of genomic regions. It provides set operations like union, intersection, difference or membership tests. Specific data types are also provided when the regions are annotated with some value.

Genomic regions are represented as a pair formed by a range and an abstract representation of a sequence/chromosome identifier. The data structures implemented here are parameterized over this abstract type. To obtain an implementation for the most common case where chromosomes are identified with a string, simply apply the functor Make on the String module.

The functor Make provides four datatypes, which corresponds to variants where:

the regions in the set can overlap or not

the regions are annotated with some values

module Biocaml_genomeMap:

sig

module type Chromosome =

sig

type t

val compare : t -> t -> int

end

An abstract representation of a chromosome identifier

module Make: functor (Chromosome : Chromosome ) ->

sig

type range = Biocaml_range.t

type location = Biocaml_genomeMap.Chromosome.t * range

A collection of non-overlapping regions (e.g. a set of CpG islands)

module Selection:

sig

type t

val inter  : t ->
 t -> t

val union  : t ->
 t -> t

val diff  : t ->
 t -> t

val size  : t -> int

val intersects  : t -> Biocaml_genomeMap.Make.location -> bool

intersects loc sel returns true if loc has a non-empty intersection with sel, and false otherwise.

val overlap  : t -> Biocaml_genomeMap.Make.location -> int

val to_stream  : t ->
 Biocaml_genomeMap.Make.location Stream.t

val of_stream  : Biocaml_genomeMap.Make.location Stream.t ->
 t

of_stream e computes a selection (i.e. a set of non overlapping locations) as the union of the locations contained in e

end

module type Signal =

sig

type 'a t

val eval : 'a t ->
 default:'a -> Biocaml_genomeMap.Chromosome.t -> int -> 'a

function evaluation at some point in the genome

val fold : 'a t ->
 init:'c -> f:('c -> Biocaml_genomeMap.Make.location -> 'b -> 'c) -> 'c

folds on constant intervals of the function, in increasing order

val to_stream : 'a t ->
 (Biocaml_genomeMap.Make.location * 'a) Stream.t

stream over all constant intervals of the function, in increasing order

val of_stream : ('a -> 'a -> 'a) ->
 (Biocaml_genomeMap.Make.location * 'a) Stream.t ->
 'a t

of_stream f ls builds a signal from a collection of annotated locations. f is used when two locations intersect, to compute the annotation on their intersection. *Beware*, f should be associative and commutative since when many locations in ls intersect, there is no guarantee on the order followed to aggregate them and their annotation.

end

Partial function over the genome (e.g.

A set of locations (e.g. a set of gene loci)

module LSet:

sig

type t

val to_stream  : t -> Biocaml_genomeMap.Make.location Stream.t

val of_stream  : Biocaml_genomeMap.Make.location Stream.t -> t

val intersects  : t -> Biocaml_genomeMap.Make.location -> bool

intersects lset loc returns true if loc has a non-empty intersection with one of the locations in lset, and returns false otherwise

val closest  : t ->
 Biocaml_genomeMap.Make.location ->
 (Biocaml_genomeMap.Make.location * int) option

closest lset loc returns the location in lset that is the closest to loc, along with the actual (minimal) distance. Returns None if there is no location in lset that comes from the same chromosome than loc.

val intersecting_elems  : t ->
 Biocaml_genomeMap.Make.location -> Biocaml_genomeMap.Make.location Stream.t

intersecting_elems lset loc returns a stream of all locations in lset that intersect loc.

end

A set of locations with an attached value on each of them

module LMap:

sig

type 'a t

val to_stream  : 'a t ->
 (Biocaml_genomeMap.Make.location * 'a) Stream.t

val of_stream  : (Biocaml_genomeMap.Make.location * 'a) Stream.t ->
 'a t

val intersects  : 'a t -> Biocaml_genomeMap.Make.location -> bool

intersects lmap loc returns true if loc has a non-empty intersection with one of the locations in lmap, and returns false otherwise

val closest  : 'a t ->
 Biocaml_genomeMap.Make.location ->
 (Biocaml_genomeMap.Make.location * 'a * int) option

closest lmap loc returns the location in lmap that is the closest to loc, along with its annotation and the actual (minimal) distance. Returns None if there is no location in lmap that comes from the same chromosome than loc.

val intersecting_elems  : 'a t ->
 Biocaml_genomeMap.Make.location ->
 (Biocaml_genomeMap.Make.location * 'a) Stream.t

intersecting_elems lmap loc returns a stream of elements in lmap whose location intersects with loc.

end