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

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

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

via ARC Commander
via git

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arc get --nolfs -r https://git.nfdi4plants.org/brilator/Facultative-CAM-in-Talinum.git

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GIT_LFS_SKIP_SMUDGE=1 git clone --filter=blob:none https://git.nfdi4plants.org/brilator/Facultative-CAM-in-Talinum.git

Preparation

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

FSharp
Python

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#r "nuget: ARCtrl"
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#r "nuget: ARCtrl.QueryModel"
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open ARCtrl
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open ARCtrl.QueryModel
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open ARCtrl.Json
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open System.IO
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// Path to a local ARC
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let arcPath = @"Facultative-CAM-in-Talinum"
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// Load local ARC from scaffold
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let arc = ARC.load arcPath
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// Store the ArcInvestigation object for easier access
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let investigation = arc.ISA.Value

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from arctrl.arc import ARC
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from arctrl.arctrl import  JsonController
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import json
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# Path to a local ARC
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arcPath = "Facultative-CAM-in-Talinum"
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# Load local ARC from scaffold
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arc = ARC.load(arcPath)
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# Store the ArcInvestigation object for easier access
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investigation = arc.ISA

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.

FSharp
Python

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// Function to export a selected study to a .json file
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let exportStudyToJson (a: ArcInvestigation) (studyIdentifier : string) =
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  a.GetStudy studyIdentifier
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  |> ArcStudy.toJsonString 2
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  |> fun c -> File.WriteAllText(studyIdentifier + ".arctrl.json", c)
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// Print all study identifiers
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investigation.StudyIdentifiers |> Seq.iter (printfn "%s")
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  // TalinumGenomeDraft
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  // TalinumSamples-STRI
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  // val it: unit = ()
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exportStudyToJson investigation "TalinumSamples-STRI"

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# Function to export a selected study to a .json file
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def exportStudyToJson (arcInvestigation, studyIdentifier):
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    study = arcInvestigation.GetStudy (studyIdentifier)
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    studyJson = JsonController.Study().to_json_string(study, spaces = 2)
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    with open(studyIdentifier + ".arctrl.json", 'w') as f:
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        f.write(studyJson)
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# Print all study identifiers
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print (*investigation.StudyIdentifiers, sep='\n')
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  # TalinumGenomeDraft
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  # TalinumSamples-STRI
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exportStudyToJson (investigation, "TalinumSamples-STRI")

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.

FSharp
Python

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// Function to export a selected assay to a .json file
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let exportAssayToJson (a: ArcInvestigation) (assayIdentifier : string) =
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  a.GetAssay assayIdentifier
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  |> ArcAssay.toJsonString 2
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  |> fun c -> File.WriteAllText(assayIdentifier + ".arctrl.json", c)
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// Print all assay identifiers
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investigation.AssayIdentifiers |> Seq.iter (printfn "%s")
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  // MassHunter_targets
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  // RNASeq
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  // GCqTOF_targets
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  // val it: unit = ()
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exportAssayToJson investigation "RNASeq"

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# Function to export a selected assay to a .json file
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def exportAssayToJson (arcInvestigation, assayIdentifier):
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    assay = arcInvestigation.GetAssay (assayIdentifier)
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    assayJson = JsonController.Assay().to_json_string(assay, spaces = 2)
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    with open(assayIdentifier + ".arctrl.json", 'w') as f:
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        f.write(assayJson)
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# Print all assay identifiers
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print(*investigation.AssayIdentifiers, sep='\n')
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  # MassHunter_targets
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  # RNASeq
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  # GCqTOF_targets
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exportAssayToJson (investigation, "RNASeq")

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.

FSharp

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let exportArcTableToJson (a: ArcInvestigation) (tableName : string) =
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  let at = investigation.ArcTables
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  at.GetTable tableName
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  |> ArcTable.toJsonString 2
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  |> fun c -> File.WriteAllText(tableName + ".arctrl.json", c)
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// Print all Table Names
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investigation.ArcTables.TableNames |> Seq.iter (printfn "%s")
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  // val it: string list =
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  // ["TalinumGenomeDraft"; "plant_material"; "mh-quant-results";
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  //  "mh-quant-report"; "rna_extraction"; "illumina"; "metabolite_extraction";
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  //  "gas_chromatography"; "mass_spec"]
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exportArcTableToJson investigation "rna_extraction"

Download example

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