21 releases
0.2.14 | Oct 17, 2024 |
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0.2.13 | Oct 3, 2024 |
0.2.12 | Jan 3, 2024 |
0.2.11 | Oct 24, 2023 |
0.1.8 | Jul 21, 2022 |
#179 in Biology
174 downloads per month
Used in 5 crates
56KB
1K
SLoC
fxread
A barebones fastx reader for rust.
Summary
This crate attempts to be a faster and more lightweight alternative to bio-rs
and provides a standardized interface to working with fasta and fastq formats.
The goal of this crate is to be fast and flexible - it is about twice as fast as bio-rs
on average but about half as fast than fastq
for standard fastx files.
The difference between the different crates is reduced heavily though once gzip files are included (see benchmark).
The speed up can be attributed to reducing the total number of vectors allocated for each record - but the limitation compared to fastq
is that each record has ownership over its data and is allocated once.
This creates extra overhead, but is very convenient as you can treat the reader directly as an iterator.
Usage
Some benefits of this interface is that each FastaReader
and FastqReader
share the FastxReader
trait and act as iterators over Record
s.
initialize_reader
can determine the fastq format from the path name
use fxread::initialize_reader;
let path = "example/sequences.fq";
let reader = initialize_reader(path).unwrap();
assert_eq!(reader.count(), 10);
initialize_reader
can handle if the file is gzip or not without changing the downstream usage
use fxread::initialize_reader;
let path = "example/sequences.fq.gz";
let reader = initialize_reader(path).unwrap();
assert_eq!(reader.count(), 10);
Check out the API Documentation for usage
Dependencies
~4MB
~74K SLoC