package biocaml

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in-package search v0.2.0

The OCaml Bioinformatics Library

Install

Dune Dependency

github.com Readme Edit opam file Versions (5)

Authors

Maintainers

P

philippe.veber@gmail.com

Sources

biocaml-0.11.2.tbz

sha256=fae219e66db06f81f3fd7d9e44717ccf2d6d85701adb12004ab4ae6d3359dd2d

sha512=f6abd60dac2e02777be81ce3b5acdc0db23b3fa06731f5b2d0b32e6ecc9305fe64f407bbd95a3a9488b14d0a7ac7c41c73a7e18c329a8f18febfc8fd50eccbc6

doc/biocaml.base/Biocaml_base/Gff/index.html

Module `Biocaml_base.Gff`Source

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

Sourcetype 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.

Sourcetype item = [

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

]

The items being output by the parser.

Source

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