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How to use

The data model library provides access to different sequencer and bioinformatic pipeline output schemas in JSON that have been defined in collaboration with the labs.

Overview:

Create object

Nanopore experiment output

In order to create an instance of type OxfordNanoporeExperiment, you need to provide a map that provides content following the Nanopore Instrument Output Schema JSON.
Every measurement folder also needs to be enriched with metadata, which itself is specified with another JSON schema.

The final map contains an additional metadata property for each measurement, that for example can look like this:

{
    "name": "QABCD001AB_E12A345a01_PAE12345",
    "path": "./",
    "children": [
        {
            "name": "20200122_1217_1-A1-B1-PAE12345_1234567a",
            "metadata":  {
                "adapter": "flongle",
                "asic_temp": "32.631687",
                "base_caller": "Guppy",
                "base_caller_version": "3.2.8+bd67289",
                "device_type" : "promethion",
                "flow_cell_id": "PAE26306",
                "flow_cell_product_code": "FLO-PRO002",
                "flow_cell_position": "2-A3-D3",
                "hostname": "PCT0094",
                "protocol": "sequencing/sequencing_PRO002_DNA:FLO-PRO002:SQK-LSK109:True",
                "started": "2020-02-11T15:52:10.465982+01:00"
            },
            "path": "./20200122_1217_1-A1-B1-PAE12345_1234567a",
            ...
            ]
}

The data model API outlines how to create an instance of OxfordNanoporeExperiment.

Nf-Core dataset

In order to create an instance of type NfCorePipelineResult, you need to provide a map that provides content following the Nfcore Pipeline Output Schema JSON.

The data model API outlines how to create an instance of NfCorePipelineResult.

MaxQuant dataset

In order to create an instance of type MaxQuantRunResult, you need to provide a map that provides content following the MaxQuant Schema JSON.

The data model API outlines how to create an instance of MaxQuantRunResult.

Validate data structure

Each object contains a schema within which can be used to test if a parsed file tree conforms to the expected structure.
The validation itself is performed via the SchemaLoader class provided by the Everit package.

Usage examples

OxfordNanoporeExperiment is used in the core utils API. Usage examples can also be seen in the associated unit test.

NfCorePipelineResult is used in the core utils API. Usage examples can also be seen in the associated unit test.

MaxQuantRunResult is used in the core utils API. Usage examples can also be seen in the associated unit test.