illumina_array_reader

A rust library to read Illumina Idat files. A port of illuminaio.

How to implement in your project

Add this line to you Cargo.toml within the [dependencies] section:
illumina_array_reader = {git = "https://github.com/a-xavier/illumina_array_reader.git"}

How to use

illumina_array_reader implements two structs MicroArray and Idat. In practice, one would only need to use MicroArray since it's a collection of a red and a green Idat.

Each Idat struct contains descriptions and most importantly, a data field containing a polars DataFrame with the data contained in the idat (ProbeID, Mean fluorescence, Fluorescence Standard Deviation and Number of beads).

To load an array, just provide a Basename. A Basename is the path to both idat files, without the _Grn.idat or _Grn.idat.gz.

For example:

use illumina_array_reader::array::MicroArray;
fn main() {
    let array = MicroArray::from_base("/path/to/files/203952880120_R01C01");

    dbg!(array);
}

Will print:

MicroArray::from_base(all_idats[0]) = MicroArray {
    basename: "/path/to/files/203952880120_R01C01",
    green_idat: Idat {
        pathname: "/path/to/files/203952880120_R01C01_Grn.idat",
        is_red: false,
        is_green: true,
        processed: true,
        is_valid_idat: true,
        total_number_of_beads: 1051815,
        barcode: "203952880120",
        position: "R01C01",
        data: shape: (1_051_815, 4)
        ┌──────────┬───────┬──────┬─────────┐
        │ ID       ┆ Mean  ┆ SD   ┆ N_beads │
        │ ---      ┆ ---   ┆ ---  ┆ ---     │
        │ u32      ┆ u16   ┆ u16  ┆ u8      │
        ╞══════════╪═══════╪══════╪═════════╡
        │ 1600101  ┆ 10409 ┆ 1275 ┆ 14      │
        │ 1600111  ┆ 5754  ┆ 302  ┆ 10      │
        │ 1600115  ┆ 2539  ┆ 442  ┆ 19      │
        │ 1600123  ┆ 5540  ┆ 703  ┆ 20      │
        │ …        ┆ …     ┆ …    ┆ …       │
        │ 99810970 ┆ 98    ┆ 38   ┆ 6       │
        │ 99810978 ┆ 7953  ┆ 412  ┆ 17      │
        │ 99810990 ┆ 5474  ┆ 735  ┆ 9       │
        │ 99810992 ┆ 4181  ┆ 508  ┆ 25      │
        └──────────┴───────┴──────┴─────────┘,
        chip_type: "BeadChip 8x5",
    },
    red_idat: Idat {
        pathname: "/path/to/files/203952880120_R01C01_Red.idat",
        is_red: true,
        is_green: false,
        processed: true,
        is_valid_idat: true,
        total_number_of_beads: 1051815,
        barcode: "203952880120",
        position: "R01C01",
        data: shape: (1_051_815, 4)
        ┌──────────┬───────┬──────┬─────────┐
        │ ID       ┆ Mean  ┆ SD   ┆ N_beads │
        │ ---      ┆ ---   ┆ ---  ┆ ---     │
        │ u32      ┆ u16   ┆ u16  ┆ u8      │
        ╞══════════╪═══════╪══════╪═════════╡
        │ 1600101  ┆ 4648  ┆ 923  ┆ 14      │
        │ 1600111  ┆ 4382  ┆ 1110 ┆ 10      │
        │ 1600115  ┆ 27623 ┆ 2773 ┆ 19      │
        │ 1600123  ┆ 3322  ┆ 652  ┆ 20      │
        │ …        ┆ …     ┆ …    ┆ …       │
        │ 99810970 ┆ 2627  ┆ 806  ┆ 6       │
        │ 99810978 ┆ 5296  ┆ 947  ┆ 17      │
        │ 99810990 ┆ 15208 ┆ 1883 ┆ 9       │
        │ 99810992 ┆ 728   ┆ 458  ┆ 25      │
        └──────────┴───────┴──────┴─────────┘,
        chip_type: "BeadChip 8x5",
    },
}

To Do

• Clean up the code and remove all .unwrap() calls -> Properly handle errors
• Create Errors
• Eliminate need for SD and N_Beads to reduce space
• Set up tests