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

v0.10.0.tar.gz
md5=497e3f2f7128a6ca347d66848da38a3d
sha512=4a76ebbafda3bc944afaff40d69791dfe153a0638ef5d7e6e1bc962b7f991d9545cd0af2d7930b39f8b31dbf067d0603cfa03d9b7a49396ab1ae452df47fd1f3

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

Module Biocaml_unix.Wig

WIG data.

Internal representation of coordinates always assumes the first position on a chromosome is numbered 1. Also, integer ranges are always closed; the range [1, 10] is the set of integers from 1 to 10 inclusive of 1 and 10. WIG data can be in three formats---bed, variable-step, or fixed-step---and unfortunately each has different conventions as follows:

  • Bed format requires half-open intervals [low, high\) and numbers the first base as 0. Thus 1 is added to the low value when parsing. The line "chrI 0 10 3.14" is parsed to ("chrI", 1, 10, 3.14).
  • Variable-step format numbers the first position 1 and uses closed intervals. Thus no change is required. The line "1 3.14" is parsed to (1, 3.14).
  • Fixed-step format numbers the first position 1 and uses closed intervals. Thus no change is required. The header line "fixedStep chrom=chrI start=1 step=100 span=30" is parsed to ("chrI", 1, 100, 30).

The inverse is done for printing routines. You are freed from these details if you always use this module to parse and print.

All parsers allow columns (fields) on a line to be separated by any combination of space, tab, or carriage return characters. Printers always separate columns with a single tab. Tag-value pairs must be in the form "tag=value" with no space around the '='.

Basic Types

type comment = [
  1. | `comment of string
]
type variable_step = [
  1. | `variable_step_state_change of string * int option
  2. | `variable_step_value of int * float
]

variable_step_state_change of name x span

type fixed_step = [
  1. | `fixed_step_state_change of string * int * int * int option
  2. | `fixed_step_value of float
]

fixed_step_state_change of name, start, step, span

type bed_graph_value = string * int * int * float
type item = [
  1. | comment
  2. | variable_step
  3. | fixed_step
  4. | `bed_graph_value of bed_graph_value
]

The most general type that the default parser outputs.

type t = [comment | variable_step | fixed_step | `bed_graph_value of bed_graph_value ]

Error Types

module Error : sig ... end

The errors of the Wig module.

Tags

module Tags : sig ... end

In_channel Functions

exception Error of Error.t
val in_channel_to_item_stream : ?buffer_size:int -> ?filename:string -> ?tags:Tags.t -> Core_kernel.In_channel.t -> (item, Error.t) Core_kernel.result Stream.t

Get a stream of item values out of an input-channel.

val in_channel_to_item_stream_exn : ?buffer_size:int -> ?filename:string -> ?tags:Tags.t -> Core_kernel.In_channel.t -> item Stream.t

Do like in_channel_to_item_stream but each call to Stream.next may throw an exception.

val in_channel_to_bed_graph : ?buffer_size:int -> ?filename:string -> ?tags:Tags.t -> Core_kernel.In_channel.t -> (bed_graph_value, Error.t) Core_kernel.result Stream.t

Get a stream of bed_graph_value values out of a WIG-file input-channel.

val in_channel_to_bed_graph_exn : ?buffer_size:int -> ?filename:string -> ?tags:Tags.t -> Core_kernel.In_channel.t -> bed_graph_value Stream.t

Do like in_channel_to_bed_graph but each call to Stream.next may throw an exception.

To_string Functions

val item_to_string : ?tags:Tags.t -> item -> string

Convert an item to a string (including new line characters).

Note: the parsing of the Tags.t is staged, so storing let to_string = item_to_string ~tags only once could be slightly more efficient than calling item_to_string ~tags item many times.

Transform Creations

module Transform : sig ... end

Low-level Tfxm.t.

S-Expressions

val comment_of_sexp : Sexplib.Sexp.t -> comment
val sexp_of_comment : comment -> Sexplib.Sexp.t
val variable_step_of_sexp : Sexplib.Sexp.t -> variable_step
val sexp_of_variable_step : variable_step -> Sexplib.Sexp.t
val fixed_step_of_sexp : Sexplib.Sexp.t -> fixed_step
val sexp_of_fixed_step : fixed_step -> Sexplib.Sexp.t
val bed_graph_value_of_sexp : Sexplib.Sexp.t -> bed_graph_value
val sexp_of_bed_graph_value : bed_graph_value -> Sexplib.Sexp.t
val item_of_sexp : Sexplib.Sexp.t -> item
val sexp_of_item : item -> Sexplib.Sexp.t