Crate fxread

Summary

This is a package to handle reading of fastx records.

fastx records are defined from fasta or fastq formats but a fastx record is one with an id and sequence regardless of its input format.

This package defines the FastxRead trait, which is implemented by both FastaReader and FastqReader. This trait allows these types to be treated as an Iterator which returns a fastx Record on each next().

This package also handles the creation of a FastxRead capable reader from the naming of an input file using dynamic dispatch. This utility is found in initialize_reader. Please see usage for example usages or each items unit tests.

Usage

Reading from a file directly

This is a very common usecase, where you have some file you’d like to read records from directly. Check out this function directly for more examples.

use fxread::initialize_reader;
let path = "example/sequences.fa";
let reader = initialize_reader(path).unwrap();
reader
    .for_each(|record| println!("{:?}", record));

Re-exports

• pub use fasta::FastaReader;
• pub use fastq::FastqReader;
• pub use fastx::FastxRead;
• pub use record::Record;
• pub use utils::initialize_reader;
• pub use utils::initialize_stdin_reader;

Modules

• fasta
  Module for a fasta reader
• fastq
  Module for a fastq reader
• fastx
  Module for the fastxread trait
• record
  Module for fastx records.
• utils
  Module for utility functions associated with creating the correct fastx reader.