pub fn initialize_reader(
    path: &str
) -> Result<Box<dyn FastxRead<Item = Record>>>
Expand description

Initializing a reader dependent on the file path extensions.

Recognized Extensions

This recognizes FASTA formats from *.fa and *.fasta and FASTQ formats from *.fq and *.fastq. These will then be opened with gzip buffers or standard depending on if the *.gz extension is found at the end of the pathname.

From Fasta

This example shows the creation of a reader from a fasta formatted plaintext file.

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

From Gzip Fasta

A common problem for the above however is that your file may actually be gzipped. Here you can use the same function and it will handle the initialization of the reader depending on the extension.

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

From Fastq

Here is another example for a fastq-formatted file that is plaintext

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

From Gzip Fastq

Here is another example for a fastq-formatted file that is gzipped

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