https://github.com/euphrasiologist/trfr

Parse output from tandem repeat finder
https://github.com/euphrasiologist/trfr

Last synced: 12 days ago
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Parse output from tandem repeat finder

• Host: GitHub
• URL: https://github.com/euphrasiologist/trfr
• Owner: Euphrasiologist
• License: mit
• Created: 2024-01-21T21:27:04.000Z (almost 1 year ago)
• Default Branch: main
• Last Pushed: 2024-01-22T14:53:54.000Z (12 months ago)
• Last Synced: 2024-04-24T08:29:23.514Z (9 months ago)
• Language: Rust
• Size: 18.6 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# `trfr`

The `trfr` crate is purely for parsing the output of the command line tool `Tandem Repeat Finder` (or `trf`).

The output is generated by passing the `-d` flag to createa parseable table (rather than the standard HTML output). Please see [here](https://github.com/Benson-Genomics-Lab/TRF) for the source code and citation for `trf`.

The API follows that of most mainstream Rust API's (in particular BurntSushi's). It is an iterator API.

# Example

```rust

use std::{error::Error, io, process};

fn example() -> Result<(), Box> {

    // Build the trfr reader

    // and assuming you are parsing with `-d` flag only

    let mut rdr = trfr::Reader::from_reader(io::stdin(), trfr::Flag::D);

    for result in rdr.records() {

        let record = result?;

        println!("{:?}", record);

    }

    Ok(())

}

fn main() {

    if let Err(err) = example() {

        println!("error running example: {}", err);

        process::exit(1);

    }

}

```