package biotk

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biotk.pipes.unix
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General Feature Format

This is a module to handle the General Feature Format, a widely-used file format to represent transcriptome annotations. There are two versions of it currently in use, GFF2 (also known as GTF) and GFF3 (most often called GFF). They differ at the syntax level in the encoding of attributes (see below) and GFF3 introduces other, more semantic, differences (see this summary).

see http://gmod.org/wiki/GFF3

see http://gmod.org/wiki/GFF2

see https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md

see https://www.ensembl.org/info/website/upload/gff.html

see https://agat.readthedocs.io/en/latest/gxf.html#the-gtf-gff-formats

module Record : sig ... end

val record : 
  ?source:string ->
  ?feature:string ->
  ?score:float ->
  ?strand:[ `Plus | `Minus | `Not_stranded | `Unknown ] ->
  ?phase:int ->
  ?attributes:(string * string list) list ->
  string ->
  int ->
  int ->
  Record.t

type item = [

| `Comment of string
| `Record of Record.t

]

module type S = sig ... end

module GFF2 : S

module GFF3 : S

val angstrom_parser : [ `gff2 | `gff3 ] -> item list Angstrom.t

module Annotation : sig ... end