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Export annotation Tables from ARCs

This guide demonstrates how to use ARCtrl to export annotation tables from an ARC into individual json files.

Use-case

Section titled Use-case

Some users want to quickly export studies, assays or individual annotation tables into easily shareable and reusable json files. This might help to establish SOPs from a lab-typical ARC.

Example script

Section titled Example script

To follow this example you can download the public ARC Facultative-CAM-in-Talinum and store it parallel to the script.

Preparation

Section titled Preparation

First, load the required libraries and load the local ARC into an ArcInvestigation object for easy access.

export-tables.fsx
#r "nuget: ARCtrl"
#r "nuget: ARCtrl.QueryModel"


open ARCtrl
open ARCtrl.QueryModel
open ARCtrl.Json
open System.IO


// Path to a local ARC


let arcPath = @"Facultative-CAM-in-Talinum"


// Load local ARC from scaffold


let arc = ARC.load arcPath


// Store the ArcInvestigation object for easier access
let investigation = arc.ISA.Value

Export a study

Section titled Export a study

We can simply create a function exportStudyToJson, which takes an ArcInvestigation object and a selected study identifier as inputs and writes the json (of type ARCtrl json) to a file named by the study identifier with the extension “.arctrl.json”. In this example, we select “TalinumSamples-STRI” from the available studies.

export-tables.fsx
let exportStudyToJson (a: ArcInvestigation) (studyIdentifier : string) =
  a.GetStudy studyIdentifier
  |> ArcStudy.toJsonString 2
  |> fun c -> File.WriteAllText(studyIdentifier + ".arctrl.json", c)


// Print all study identifiers


investigation.StudyIdentifiers |> Seq.iter (printfn "%s")


  // TalinumGenomeDraft
  // TalinumSamples-STRI
  // val it: unit = ()


exportStudyToJson investigation "TalinumSamples-STRI"

Export an assay

Section titled Export an assay

In the same manner, we can create a function exportAssayToJson, which takes an ArcInvestigation object and a selected assay identifier as inputs and writes the json (of type ARCtrl json) to a file named by the assay identifier with the extension “.arctrl.json”. In this example, we select “RNASeq” from the available assays.

export-tables.fsx
let exportAssayToJson (a: ArcInvestigation) (assayIdentifier : string) =
  a.GetAssay assayIdentifier
  |> ArcAssay.toJsonString 2
  |> fun c -> File.WriteAllText(assayIdentifier + ".arctrl.json", c)


// Print all assay identifiers


investigation.AssayIdentifiers |> Seq.iter (printfn "%s")


  // MassHunter_targets
  // RNASeq
  // GCqTOF_targets
  // val it: unit = ()


exportAssayToJson investigation "RNASeq"

Export a single table

Section titled Export a single table

Instead of exporting a full study or assay, including all annotation tables and the respective metadata sheet, respectively, you can also export a single annotation table.

export-tables.fsx
let exportArcTableToJson (a: ArcInvestigation) (tableName : string) =
  let at = investigation.ArcTables
  at.GetTable tableName
  |> ArcTable.toJsonString 2
  |> fun c -> File.WriteAllText(tableName + ".arctrl.json", c)


// Print all Table Names


investigation.ArcTables.TableNames |> Seq.iter (printfn "%s")


  // val it: string list =
  // ["TalinumGenomeDraft"; "plant_material"; "mh-quant-results";
  //  "mh-quant-report"; "rna_extraction"; "illumina"; "metabolite_extraction";
  //  "gas_chromatography"; "mass_spec"]


exportArcTableToJson investigation "rna_extraction"

Download example

Section titled Download example

You can download the example script to adapt it to your needs.