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#![crate_name = "needletail"]
//! Needletail is a crate to quickly and easily parse FASTA and FASTQ 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_fastx_file, Sequence, FastxReader};
//!
//! fn main() {
//! let filename = "tests/data/28S.fasta";
//!
//! let mut n_bases = 0;
//! let mut n_valid_kmers = 0;
//! let mut reader = parse_fastx_file(&filename).expect("valid path/file");
//! while let Some(record) = reader.next() {
//! let seqrec = record.expect("invalid record");
//! // keep track of the total number of bases
//! n_bases += seqrec.num_bases();
//! // normalize to make sure all the bases are consistently capitalized and
//! // that we remove the newlines since this is FASTA
//! let norm_seq = seqrec.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 position (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;
//! }
//! }
//! }
//! println!("There are {} bases in your file.", n_bases);
//! println!("There are {} AAAAs in your file.", n_valid_kmers);
//! }
//! ```
//!
#[cfg(any(feature = "python", feature = "python_test"))]
extern crate pyo3;
pub mod bitkmer;
pub mod kmer;
pub mod parser;
pub mod sequence;
pub mod errors;
#[cfg(any(feature = "python", feature = "python_test"))]
pub mod python;
pub use parser::{parse_fastx_file, parse_fastx_reader, parse_fastx_stdin, FastxReader};
pub use sequence::Sequence;