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The OCaml Bioinformatics Library

Install

Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

Maintainers

B

biocaml@googlegroups.com

Sources

v0.10.0.tar.gz

md5=497e3f2f7128a6ca347d66848da38a3d

sha512=4a76ebbafda3bc944afaff40d69791dfe153a0638ef5d7e6e1bc962b7f991d9545cd0af2d7930b39f8b31dbf067d0603cfa03d9b7a49396ab1ae452df47fd1f3

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

Module `Biocaml_unix.Bed`

BED data files.

A BED file is in the format shown below, where columns must be separated by a tab character.

chrA   lo1   hi1
chrA   lo2   hi2
.      .     .
.      .     .
.      .     .
chrB   lo1   hi1
chrB   lo2   hi2
.      .     .
.      .     .
.      .     .

The definition is that intervals are zero based and half-open. So by default the line "chrA lo hi" is parsed to the interval [lo + 1, hi] on chromosome chrA. Similarly, when printing, the default is to print [lo - 1, hi]. The optional argument increment_lo_hi allows changing this behavior for non-conformant files. In addition, the optional argument chr_map is a string -> string function that allows changing of the chromosome name to a specified format, and defaults to identity.

Some tools require that the set of intervals do not overlap within each chromosome. This is not enforced, but you can use any_overlap to verify this property when needed.

Item Types

type item = string * int * int * Table.Row.t

The type of BED data stream items.

Tags: Describe The Format: TODO

type parsing_spec = [

| `enforce of Table.Row.t_type
| `strings

]

The specification of how to parse the remaining columns.

Error Types

module Error : sig ... end

Definitions of error types (with sexp)

`In_channel` Functions

exception Error of Error.t

val in_channel_to_item_stream : 
  ?buffer_size:int ->
  ?more_columns:parsing_spec ->
  Core_kernel.In_channel.t ->
  (item, [> Error.parsing ]) Core_kernel.result Stream.t

Parse an input-channel into item values.

val in_channel_to_item_stream_exn : 
  ?buffer_size:int ->
  ?more_columns:parsing_spec ->
  Core_kernel.In_channel.t ->
  item Stream.t

Like in_channel_to_item_stream but use exceptions for errors (raised within Stream.next).

Conversions to/from `Line.t`

Transforms

module Transform : sig ... end

Lower-level transforms of BED data-streams.

S-Expressions

val item_of_sexp : Sexplib.Sexp.t -> item

val sexp_of_item : item -> Sexplib.Sexp.t

val parsing_spec_of_sexp : Sexplib.Sexp.t -> parsing_spec

val sexp_of_parsing_spec : parsing_spec -> Sexplib.Sexp.t

On This Page

Item Types
Tags: Describe The Format: TODO
Error Types
In_channel Functions
Conversions to/from Line.t
Transforms
S-Expressions