Crate csvranger 

csvranger

csranger is a library for parsing the output CSV files of 10x Genomics *ranger pipelines.

Many of 10x Genomics data-processing pipelines produce CSV files that summarize the data. These CSVs, while human-readable, cannot be parsed by a machine without extra effort. This small crate provides the necessary functionality to parse the values in these files. See documentation at csvranger.

Example usage

Using TenxCsvValue::from_csv_value

use csvranger::TenxCsvValue;

fn main() {
    // Sample data from test-data/cellranger_multi.10.0
    let raw_csv = b"Sample ID,Sample barcodes,Sample description,GEX: Cells,GEX: Confidently mapped reads in cells,GEX: Median UMI counts per cell,GEX: Median genes per cell,GEX: Total genes detected
    SOD1_G93A_mouse_spinal_cord_P112_specimen_1,,SOD1-G93A mouse spinal cord from P112 mouse,16410,0.6847850295990157,2244,1305,27219";

    let mut reader = csv::Reader::from_reader(&raw_csv[..]);
    for line in reader.records() {
        // Don't actually call .unwrap in production!
        let line = line.unwrap();
        for value in line.iter() {
            // This is where the magic happens
            TenxCsvValue::from_csv_value(value);
        }
    }
}

Deserializing directly

use csvranger::TenxCsvValue;
use std::collections::HashMap;

fn main() {
    // Sample data from test-data/cellranger_multi.10.0
    let raw_csv = b"Sample ID,Sample barcodes,Sample description,GEX: Cells,GEX: Confidently mapped reads in cells,GEX: Median UMI counts per cell,GEX: Median genes per cell,GEX: Total genes detected
    SOD1_G93A_mouse_spinal_cord_P112_specimen_1,,SOD1-G93A mouse spinal cord from P112 mouse,16410,0.6847850295990157,2244,1305,27219";

    let mut reader = csv::Reader::from_reader(&raw_csv[..]);
    let mut parsed_data: Vec<HashMap<String, TenxCsvValue>> = Vec::new();

    #[cfg(feature = "serde")]
    for deserialized_record in reader.deserialize() {
        parsed_data.push(deserialized_record.unwrap())
    }
}

Enums

TenxCsvValue

A CSV value found in the metrics_summary.csv files produced by 10x Genomics *ranger pipelines.

Functions

parse_legacy_csv_value_as_f64

Parse a value in a CSV outputted by a legacy 10x Genomics pipeline as an f64.

parse_legacy_csv_value_as_i64

Parse a value in a CSV outputted by a legacy 10x Genomics pipeline as an i64.