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.base/Biocaml_base/Gff/index.html

Module `Biocaml_base.Gff`

GFF files.

Versions 2 and 3 are supported. The only difference is the delimiter used for tag-value pairs in the attribute list: 3 uses an equal sign, and 2 uses a space. Version 3 also has additional requirements, e.g. the feature must be a sequence ontology term, but these are not checked.

More information:

Version 2: www.sanger.ac.uk/resources/software/gff/spec.html, gmod.org/wiki/GFF2
Version 3: www.sequenceontology.org/gff3.shtml, gmod.org/wiki/GFF3

GFF Item Types

type record = {

seqname : Base.string;
source : Base.string Base.option;
feature : Base.string Base.option;
start_pos : Base.int;
stop_pos : Base.int;
score : Base.float Base.option;
strand : [ `Plus | `Minus | `Not_stranded | `Unknown ];
phase : Base.int Base.option;
attributes : (Base.string * Base.string Base.list) Base.list;

}

The type of the GFF records/rows.

type item = [

| `Comment of Base.string
| `Record of record

]

The items being output by the parser.

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

val gff3_item_of_line : 
  Line.t ->
  (item, [> `Msg of Base.string ]) Base.Result.t

val gtf_item_of_line : Line.t -> (item, [> `Msg of Base.string ]) Base.Result.t

val line_of_item : [ `two | `three ] -> item -> Line.t

On This Page

GFF Item Types