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#![crate_name = "needletail"]
//! Needletail is a crate to quickly and easily parse sequences out of
//! streams/files and manipulate and analyse that data.
//!
//! A contrived example of how to use it:
//! ```
//! extern crate needletail;
//! use needletail::{parse_sequence_path, Sequence};
//! use std::env;
//!
//! fn main() {
//!     let filename = "tests/data/28S.fasta";
//!     // you could also read the filename from the command arguments like:
//!     // let filename: String = env::args().nth(1).unwrap();
//!
//!     let mut n_bases = 0;
//!     let mut n_valid_kmers = 0;
//!     parse_sequence_path(
//! 	filename,
//!         |_| {},
//!         |seq| {
//!             // seq.id is the name of the record
//!             // seq.seq is the base sequence
//!             // seq.qual is an optional quality score
//!
//!             // keep track of the total number of bases
//!             n_bases += seq.seq.len();
//!
//!             // normalize to make sure all the bases are consistantly capitalized
//!             let norm_seq = seq.normalize(false);
//!             // we make a reverse complemented copy of the sequence first for
//!             // `canonical_kmers` to draw the complemented sequences from.
//!             let rc = norm_seq.reverse_complement();
//!             // now we keep track of the number of AAAAs (or TTTTs via
//!             // canonicalization) in the file; note we also get the postion (i.0;
//!             // in the event there were `N`-containing kmers that were skipped)
//!             // and whether the sequence was complemented (i.2) in addition to
//!             // the canonical kmer (i.1)
//!             for (_, kmer, _) in norm_seq.canonical_kmers(4, &rc) {
//!                 if kmer == b"AAAA" {
//!                     n_valid_kmers += 1;
//!                 }
//!             }
//!         },
//!     )
//!     .expect("parsing failed");
//!     println!("There are {} bases in your file.", n_bases);
//!     println!("There are {} AAAAs in your file.", n_valid_kmers);
//! }
//! ```
pub mod bitkmer;
pub mod formats;
pub mod kmer;
pub mod sequence;
pub mod sequence_record;
mod util;

pub use formats::{parse_sequence_path, parse_sequence_reader};
pub use sequence::Sequence;
pub use sequence_record::SequenceRecord;
pub use util::{ParseError, ParseErrorType};