4 releases

0.1.3 Jul 8, 2023
0.1.2 Jan 10, 2023
0.1.1 Oct 12, 2022
0.1.0 Oct 7, 2022

#229 in Biology

Download history 52/week @ 2023-11-20 8/week @ 2023-11-27 21/week @ 2023-12-04 8/week @ 2024-01-08 33/week @ 2024-02-19 30/week @ 2024-02-26 21/week @ 2024-03-04

84 downloads per month
Used in 2 crates

MIT/Apache

29KB
624 lines

Yet another fasta/q/x parser

Well fuzzed though....

Benchmark

I don't know if this is correct or not, but it's fast enough. NOTE: This does not include I/O at all as that is outside the scope of this library (for now) and thus uniprot is included as a raw string in the binary.

Running benches/parse_fasta.rs (target/release/deps/parse_fasta-1e449f5527386a9a) 
Parse UniProt SwissProt FASTA File/parse_fasta 
  time: [54.788 ns 54.922 ns 55.069 ns] 
  thrpt: [4773329 GiB/s 4786111 GiB/s 4797786 GiB/s] 

Found 11 outliers among 100 measurements (11.00%)
  4 (4.00%) low mild 4 (4.00%) high mild
  3 (3.00%) high severe

Changelog

0.1.3

Pin bytelines to 2.2.2 to remove the tokio/futures dependency as it is not used here.

0.1.2

Change zlib-ng for flate2 to just zlib.


lib.rs:

Yet another rust fasta/fastq parser, with a focus on speed and memory usage. Well fuzzed and performant-focused.

The basic ones to use are fasta, fastq submodules.

The ones under zerocopy:: use slightly less memory at the cost of discontiguous streams.

Dependencies

~4.5MB
~65K SLoC