package biocaml

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The OCaml Bioinformatics Library

Install 

dune-project
 Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

  1. S
    Sebastien Mondet
  2. A
    Ashish Agarwal
  3. P
    Philippe Veber
  4. C
    Christophe Troestler
  5. S
    Sergei Lebedev
  6. D
    David Koppstein
  7. A
    Alexander Gryzlov
  8. F
    Francois Berenger

Maintainers

  1. B
    biocaml@googlegroups.com

Sources

v0.10.1.tar.gz
md5=4cf944bcae5d36bf47b67f6bcb2455d7
sha512=0262b5768aefd7c080f664c46c88876fce9a658cc6a87358a77b7112c49ae3042e7ab542e76be5738fbaeda853149b308b48d4897960b5c7ae3b4da71d978bd8

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 = [
  1. | `enforce of Table.Row.t_type
  2. | `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

The exception raised by the *_exn functions.

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

See also Line.t.

val item_of_line : how:parsing_spec -> Lines.item -> (item, [> Error.parsing ]) Core_kernel.result

Basic parsing of a single line.

val item_to_line : item -> Lines.item

Basic “printing” of one single item.

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