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

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

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

#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

from arctrl.arc import ARC
from arctrl.arctrl import  JsonController

import json

# Path to a local ARC

arcPath = "Facultative-CAM-in-Talinum"

# Load local ARC from scaffold

arc = ARC.load(arcPath)

# Store the ArcInvestigation object for easier access
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

// Function to export a selected study to a .json file

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"

# Function to export a selected study to a .json file

def exportStudyToJson (arcInvestigation, studyIdentifier):
    study = arcInvestigation.GetStudy (studyIdentifier)
    studyJson = JsonController.Study().to_json_string(study, spaces = 2)

    with open(studyIdentifier + ".arctrl.json", 'w') as f:
        f.write(studyJson)


# Print all study identifiers

print (*investigation.StudyIdentifiers, sep='\n')

  # TalinumGenomeDraft
  # TalinumSamples-STRI

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

// Function to export a selected assay to a .json file

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"

# Function to export a selected assay to a .json file

def exportAssayToJson (arcInvestigation, assayIdentifier):
    assay = arcInvestigation.GetAssay (assayIdentifier)
    assayJson = JsonController.Assay().to_json_string(assay, spaces = 2)

    with open(assayIdentifier + ".arctrl.json", 'w') as f:
        f.write(assayJson)

# Print all assay identifiers

print(*investigation.AssayIdentifiers, sep='\n')

  # MassHunter_targets
  # RNASeq
  # GCqTOF_targets

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

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

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