FastaRecord

Mojo struct 🡭

FastaRecord

@memory_only
struct FastaRecord

A single FASTA record (two logical parts: >id, sequence).

Multi-line sequences are stored as a single logical line (no embedded newlines). Owned representation; safe to store in collections and reuse.

Attributes: id: Read identifier (id line content after the ’>’; stored without leading ’>’). sequence: Sequence line (normalized to a single line, no ‘\n’ or ‘\r’).

Implemented traits

AnyType, Copyable, Hashable, ImplicitlyDestructible, Movable, Sized, Writable

Methods

__init__

def __init__(out self, id: String, sequence: String)

Build from id and sequence strings.

Args:

• id (String)
• sequence (String)
• self (Self)

Returns:

Self

Raises:

def __init__(out self, id: Span[Byte, id.origin], sequence: Span[Byte, sequence.origin])

Args:

• id (Span)
• sequence (Span)
• self (Self)

Returns:

Self

Raises:

def __init__(out self, var id: BString, var sequence: BString)

Args:

• id (BString)
• sequence (BString)
• self (Self)

Returns:

Self

__eq__

def __eq__(self, other: Self) -> Bool

Args:

• self (Self)
• other (Self)

Returns:

Bool

__ne__

def __ne__(self, other: Self) -> Bool

Args:

• self (Self)
• other (Self)

Returns:

Bool

sequence

def sequence(ref self) -> StringSlice[origin_of(self)]

Return the sequence line as a string slice.

Args:

• self (Self)

Returns:

StringSlice

id

def id(ref self) -> StringSlice[origin_of(self)]

Return the read identifier (id without leading ’>’) as a string slice.

Args:

• self (Self)

Returns:

StringSlice

definition

def definition(self) -> Definition

Args:

• self (Self)

Returns:

Definition

byte_len

def byte_len(self) -> Int

Return total byte length when written (”>” + id + “\n” + sequence + “\n”).

Args:

• self (Self)

Returns:

Int

write

def write[w: Writer](self, mut writer: w, line_width: Int = 60)

Write the record in standard FASTA format.

Parameters:

• w (Writer)

Args:

• self (Self)
• writer (w)
• line_width (Int)

write_to

def write_to[w: Writer](self, mut writer: w)

Parameters:

• w (Writer)

Args:

• self (Self)
• writer (w)

__len__

def __len__(self) -> Int

Return the sequence length (number of bases).

Args:

• self (Self)

Returns:

Int

__hash__

def __hash__[H: Hasher](self, mut hasher: H)

Parameters:

• H (Hasher)

Args:

• self (Self)
• hasher (H)

__repr__

def __repr__(self) -> String

Args:

• self (Self)

Returns:

String