Module seq_io::fasta

Efficient FASTA reading and writing

Example

This example reads some content, writes it back and compares the output (should be the same):

use seq_io::fasta::{Reader, Record};

let input = b">id1
ACGT
ACGT
>id2
TGCA
TGCA
";

let mut reader = Reader::new(&input[..]);
let mut output = vec![];

while let Some(record) = reader.next() {
    let record = record.expect("Error reading record");
    println!("id: {}", record.id().unwrap());
    record.write_wrap(&mut output, 4);
}

assert_eq!(input, output.as_slice());

Details on parsing behaviour

• The parser handles UNIX (LF) and Windows (CRLF) line endings, but not old Mac-style (CR) endings. However, FASTA writing currently always uses UNIX line endings.
• Empty lines are allowed anywhere in the file, they will just be ignored. The first non-empty line must start with >, indicating the first header.
• Whitespace at the end of header and sequence lines is never removed.
• If two consecutive FASTA header lines (starting with >) are encountered without intermediate sequence line, the first record will have an empty sequence. The same is true if the input ends with a header line.
• Empty input will result in None being returned immediately by fasta::Reader::next() and in empty iterators for RecordsIter / RecordsIntoIter.
• Comment lines starting with ; are not supported. If at the start of a file, there will be an error, since > is expected. Intermediate comments are appended to the sequence.

Structs

• OwnedRecord
  A FASTA record that ownes its data (requiring two allocations)
• Position
  Holds line number and byte offset of a FASTA record
• Reader
  Parser for FASTA files.
• RecordSet
  Set of FASTA records that owns it’P buffer and knows the positions of each record.
• RecordSetIter
  Iterator over record sets
• RecordsIntoIter
  Iterator of OwnedRecord that owns the underlying reader
• RecordsIter
  Borrowed iterator of OwnedRecord
• RefRecord
  A FASTA record that borrows data from a buffer.
• SeqLines
  Iterator over sequence the lines of a FASTA record.

Enums

• Error
  FASTA parsing error

Traits

• Record
  FASTA record trait implemented by both RefRecord and OwnedRecord

Functions

• write_head
  Writes only the sequence header.
• write_id_desc
  Writes only the sequence header given ID and description parts.
• write_parts
  Writes data to the FASTA format. ID and description parts of the header are supplied separately instead of a whole header line.
• write_seq
  Writes only the sequence line.
• write_seq_iter
  Writes the sequence line from an iterator (such as SeqLines)
• write_to
  Writes data (not necessarily stored in a Record instance) to the FASTA format.
• write_wrap
  Writes data to the FASTA format. Wraps the sequence to produce multi-line FASTA with a maximum width specified by the wrap parameter.
• write_wrap_seq
  Writes the sequence line, and wraps the output to a maximum width specified by wrap.
• write_wrap_seq_iter
  Writes the sequence line from an iterator (such as SeqLines) and wraps the output to a maximum width specified by wrap.