BioFSharp
GenBank parsing
Summary: This example shows how to parse and write genbank formatted files with BioFSharp
GenBank format
GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). A GenBank file contains various information about a sequence and its features.
The file structure of a GenBank (.gb) flat file can be split into 4 subsections:
Section |
Description |
|---|---|
Meta |
Contains meta information about the annotated sequence, the file itself and the organism the sequence is found in |
References |
A collection of publications about the annotated sequence(or a subsequence of it) and information associated with them |
Features |
A collection of features and their position within the sequence |
Origin |
The annotated sequence itself |
With the origins section being optional and the features section usually being by far the largest amongst them. For more information about the sections and their formatting, have a look at this annotated sample record over at NCBI.
This file will also be used for the purpose of this tutorial and in plain text looks like this:
|
Reading GenBank files
The type equivalent for a GenBank file in BioFSharp is a dictionary, mapping string keys to the GenBankItem<'a> type, where 'a is the type of the origin sequence in the file.
More information about the type modelling can be found in our API reference.
The default reader fromFile simply takes the origin sequence as a sequence of chars.
open BioFSharp
open BioFSharp.IO
///Path of the example file
let exampleFilePath = __SOURCE_DIRECTORY__ + @"\data\sequence.gb"
///Parsed Example File
let parsedGBFile = GenBank.Read.fromFile exampleFilePath
|
You can also use converter functions for the origin sequence, which makes it easier to use them for other BioFSharp workflows. There are multiple prebuilt converters contained in the
OriginConverters module for reading and writing. For example, the following code will parse the sequence as a BioSeq containing nucleotides
let converter = GenBank.OriginConverters.Input.nucleotideConverter
let parsedGBFile' = GenBank.Read.fromFileWithOriginConverter converter exampleFilePath
This makes it easy to perform additional tasks with the origin sequence:
let origin = GenBank.getOrigin parsedGBFile'
|
///Transcribed origin sequence
let rnaSeq = origin |> BioSeq.transcribeCodingStrand
|
///Translated origin sequence
let protein = rnaSeq |> BioSeq.translate 0
|
Writing GenBank files
Just as in the Read module, there is a default writer for a GenBank dictionary that contains a sequence of chars, as a writer taking a custom converter function. Just specify the output path, and you are ready to go.
let outputPath1 = __SOURCE_DIRECTORY__ + @"\data\sequenceTestWrite1.gb"
let outputPath2 = __SOURCE_DIRECTORY__ + @"\data\sequenceTestWrite2.gb"
let outputConverter = GenBank.OriginConverters.Output.bioItemConverter
parsedGBFile |> GenBank.Write.toFile outputPath1
parsedGBFile' |> GenBank.Write.toFileWithOriginConverter outputPath2 outputConverter
namespace BioFSharp
namespace BioFSharp.IO
val exampleFilePath: string
Path of the example file
Path of the example file
val parsedGBFile: System.Collections.Generic.Dictionary<string,GenBank.GenBankItem<char seq>>
Parsed Example File
Parsed Example File
module GenBank
from BioFSharp.IO
<summary> functions for reading and writing GenBank files </summary>
<summary> functions for reading and writing GenBank files </summary>
module Read
from BioFSharp.IO.GenBank
<summary> functions for parsing a GenBank file. </summary>
<summary> functions for parsing a GenBank file. </summary>
val fromFile: path: string -> System.Collections.Generic.Dictionary<string,GenBank.GenBankItem<char seq>>
<summary> Returns a dictionary containing GenBank items, that represents the GenBank file at the input path </summary>
<summary> Returns a dictionary containing GenBank items, that represents the GenBank file at the input path </summary>
val converter: (char seq -> BioSeq.BioSeq<Nucleotides.Nucleotide>)
module OriginConverters
from BioFSharp.IO.GenBank
<summary> contains prebuilt converters for origin sequences in a gb file for both reading and writing </summary>
<summary> contains prebuilt converters for origin sequences in a gb file for both reading and writing </summary>
module Input
from BioFSharp.IO.GenBank.OriginConverters
<summary> contains a collection of prebuilt converters for parsing specific origin sequences </summary>
<summary> contains a collection of prebuilt converters for parsing specific origin sequences </summary>
val nucleotideConverter: sequence: char seq -> BioSeq.BioSeq<Nucleotides.Nucleotide>
<summary> converts the origin sequence into a BioSeq of nucleotides </summary>
<summary> converts the origin sequence into a BioSeq of nucleotides </summary>
val parsedGBFile': System.Collections.Generic.Dictionary<string,GenBank.GenBankItem<BioSeq.BioSeq<Nucleotides.Nucleotide>>>
val fromFileWithOriginConverter: originConverter: (char seq -> 'a) -> path: string -> System.Collections.Generic.Dictionary<string,GenBank.GenBankItem<'a>>
<summary> Returns a dictionary containing GenBank items, that represents the GenBank file at the input path taking a converter function for the origin sequence of the file </summary>
<summary> Returns a dictionary containing GenBank items, that represents the GenBank file at the input path taking a converter function for the origin sequence of the file </summary>
val origin: BioSeq.BioSeq<Nucleotides.Nucleotide>
val getOrigin: gb: System.Collections.Generic.Dictionary<string,GenBank.GenBankItem<'a>> -> 'a
<summary> Returns the Origin of a GenBank file representation </summary>
<summary> Returns the Origin of a GenBank file representation </summary>
val rnaSeq: BioSeq.BioSeq<Nucleotides.Nucleotide>
Transcribed origin sequence
Transcribed origin sequence
Multiple items
module BioSeq from BioFSharp.BioCollectionsExtensions
--------------------
module BioSeq from BioFSharp
<summary> This module contains the BioSeq type and its according functions. The BioSeq type is a sequence of objects using the IBioItem interface </summary>
module BioSeq from BioFSharp.BioCollectionsExtensions
--------------------
module BioSeq from BioFSharp
<summary> This module contains the BioSeq type and its according functions. The BioSeq type is a sequence of objects using the IBioItem interface </summary>
val transcribeCodingStrand: nucs: Nucleotides.Nucleotide seq -> BioSeq.BioSeq<Nucleotides.Nucleotide>
<summary> Transcribe a given DNA coding strand (5'-----3') </summary>
<summary> Transcribe a given DNA coding strand (5'-----3') </summary>
val protein: BioSeq.BioSeq<AminoAcids.AminoAcid>
Translated origin sequence
Translated origin sequence
val translate: nucleotideOffset: int -> rnaSeq: Nucleotides.Nucleotide seq -> BioSeq.BioSeq<AminoAcids.AminoAcid>
<summary> translates nucleotide sequence to aminoacid sequence </summary>
<summary> translates nucleotide sequence to aminoacid sequence </summary>
val outputPath1: string
val outputPath2: string
val outputConverter: (BioSeq.BioSeq<#IBioItem> -> char seq)
module Output
from BioFSharp.IO.GenBank.OriginConverters
<summary> contains a collection of prebuilt converters for writing specific origin sequences </summary>
<summary> contains a collection of prebuilt converters for writing specific origin sequences </summary>
val bioItemConverter: sequence: BioSeq.BioSeq<#IBioItem> -> char seq
<summary> converts the BioSeq to the 1 letter code representing the contained items </summary>
<summary> converts the BioSeq to the 1 letter code representing the contained items </summary>
module Write
from BioFSharp.IO.GenBank
<summary> Functions for writing a GenBank file </summary>
<summary> Functions for writing a GenBank file </summary>
val toFile: path: string -> gb: System.Collections.Generic.Dictionary<string,GenBank.GenBankItem<#(char seq)>> -> unit
<summary> creates a GenBank file at the specified path </summary>
<summary> creates a GenBank file at the specified path </summary>
val toFileWithOriginConverter: path: string -> originConverter: ('a -> char seq) -> gb: System.Collections.Generic.Dictionary<string,GenBank.GenBankItem<'a>> -> unit
<summary> creates a GenBank file at the specified path, taking a converter function for the origin sequence of the file </summary>
<summary> creates a GenBank file at the specified path, taking a converter function for the origin sequence of the file </summary>