FastaParser

Mojo struct 🡭

FastaParser

@memory_only
struct FastaParser[R: Reader, config: ParserConfig = ParserConfig(False)]

Streaming FASTA parser over a Reader.

Multi-line FASTA sequences are normalised so that all line breaks within the sequence body are stripped, producing a single contiguous sequence string per record.

API: - next_record() → FastaRecord (raises EOFError when exhausted) - for rec in parser: (standard iteration, propagates parse errors — see note on _FastaParserRecordIter)

Aliases

• IteratorType[origin: Origin]: AnyStruct[_FastaParserRecordIter[R, config, origin]] = _FastaParserRecordIter[R, config, origin]

Parameters

• R (Reader)
• config (ParserConfig)

Fields

• lines (LineIterator[R])
• validator (Validator)

Implemented traits

AnyType, ImplicitlyDestructible, Iterable, Movable

Methods

__init__

def __init__(out self, var reader: R)

Args:

• reader (R)
• self (Self)

Returns:

Self

Raises:

has_more

def has_more(self) -> Bool

Return True if there may be more records to read.

Args:

• self (Self)

Returns:

Bool

get_buffer_position

def get_buffer_position(ref self) -> Int

Return the current buffer position.

Args:

• self (Self)

Returns:

Int

next_record

def next_record(mut self) -> FastaRecord

Return the next FASTA record as an owned FastaRecord.

Raises EOFError when no more records are available. Raises Error on malformed input (empty sequence, missing ’>’).

Args:

• self (Self)

Returns:

FastaRecord

Raises:

records

def records(ref self) -> _FastaParserRecordIter[R, config, origin_of(self)]

Args:

• self (Self)

Returns:

_FastaParserRecordIter

__iter__

def __iter__(ref self) -> _FastaParserRecordIter[R, config, origin_of(self)]

Args:

• self (Self)

Returns:

_FastaParserRecordIter