package biocaml

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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.ez/Biocaml_ez/Fasta/index.html

Module `Biocaml_ez.Fasta`

include module type of struct include Biocaml_unix.Fasta end

type header = private string list

A header is a list of comment lines.

type item = private Biocaml_unix.Fasta.item = {

description : string;
sequence : string;

}

type fmt = Biocaml_unix.Fasta.fmt = {

allow_sharp_comments : bool;
allow_semicolon_comments : bool;
allow_empty_lines : bool;
comments_only_at_top : bool;
max_line_length : int option;
alphabet : string option;

}

val default_fmt : fmt

Low-level Parsing

type item0 = private [<

| `Comment of string
| `Empty_line
| `Description of string
| `Partial_sequence of string

]

An item0 is more raw than item. It is useful for parsing files with large sequences because you get the sequence in smaller pieces.

`Comment _ - Single comment line without the final newline. Initial comment char is retained.

`Empty_line - Got a line with only whitespace characters. The contents are not provided.

`Description _ - Single description line without the initial '>' nor final newline.

`Partial_sequence _ - Multiple sequential partial sequences comprise the sequence of a single item.

val parse_item0 : 
  ?allow_sharp_comments:bool ->
  ?allow_semicolon_comments:bool ->
  ?allow_empty_lines:bool ->
  ?max_line_length:int ->
  ?alphabet:string ->
  Biocaml_unix.Line.t ->
  item0 Core_kernel.Or_error.t

val sequence_to_int_list : string -> int list

val read0 : 
  ?start:Biocaml_unix.Pos.t ->
  ?allow_sharp_comments:bool ->
  ?allow_semicolon_comments:bool ->
  ?allow_empty_lines:bool ->
  ?max_line_length:int ->
  ?alphabet:string ->
  Core_kernel.In_channel.t ->
  item0 CFStream.Stream.t

val read : 
  ?start:Biocaml_unix.Pos.t ->
  ?fmt:fmt ->
  Core_kernel.In_channel.t ->
  header * item CFStream.Stream.t

val with_file : 
  ?fmt:fmt ->
  string ->
  f:(header -> item CFStream.Stream.t -> 'a) ->
  'a