package biotk

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GFF 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 {http://gmod.org/wiki/GFF2#Why_GFF2_is_harmful_to_your_healththis 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 = [
  1. | `Comment of string
  2. | `Record of Record.t
]
module GFF2 : Line_oriented.S with type item := item
module GFF3 : Line_oriented.S with type item := item
val angstrom_parser : [ `gff2 | `gff3 ] -> item list Angstrom.t
module Annotation : sig ... end
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