F# BioProviders

The F# BioProviders simplify programmatic access to bioinformatics data.

This library provides strongly-typed access to over 240 million genomic sequences through a set of Type Providers, including the GenBankProvider and RefSeqProvider. For more information, see the detailed documentation.

The BioProviders work by parsing genomic data files using the .NET Bio library, which are then represented using types from the BioFSharp library.

Example

Below, a simple example of finding the complement of the genomic sequence of a Staphylococcus lugdunensis assembly is provided.

#r "nuget: BioProviders"

open BioProviders
open BioFSharp

let [<Literal>] Species = "Staphylococcus lugdunensis"
let [<Literal>] Accession = "GCA_001546615.1"

let genome = GenBankProvider<Species, Accession>.Genome()

genome.Sequence |> BioSeq.complement

The above code produces the result:

BioSeq.BioSeq<Nucleotides.Nucleotide> = seq [C; T; A; C; ...]

Building

To build the BioProviders package, perform the following steps:

• Install the .NET SDK specified in the global.json file
• build.sh -t Build or build.cmd -t Build

Creating data files

BioProviders uses a set of data files generated from assembly lists from the NCBI FTP server for species and assembly lookup.

• To generate these files, run dotnet fsi DataFileGenerator.fsx, to save the files to build\data.
  • Approximately 1 GB is required due to the download size. They are deleted on process completion; use the argument -keepDownloads to keep them.
  • To save the files in the type provider's cache folder, use the argument -saveToCache.
• By default, the package downloads files from this repository to AppData\Local\Temp\BioProviders. To change this for your own version, change the URL in the file remote.txt in src\DesignTime.

Formatting

The BioProviders package code is formatted using fantomas.

• To format the code, run build.sh -t Format or build.cmd -t Format
• To check formatting, run build.sh -t CheckFormat or build.cmd -t CheckFormat

License

BioProviders is covered by the MIT license.

The package also uses:

• BioFSharp - MIT license
• .NET Bio - Apache-2.0 license
• FluentFTP - MIT license
• FSharp.Data - Apache-2.0 license

Maintainers

Current maintainers are Alex Kenna, Samuel Smith and James Hogan.