Bio.Align.fasta module

Bio.Align support for aligned FASTA files.

Aligned FASTA files are FASTA files in which alignment gaps in a sequence are represented by dashes. Each sequence line in an aligned FASTA should have the same length.

class Bio.Align.fasta.AlignmentWriter(target)

Bases: Bio.Align.interfaces.AlignmentWriter

Alignment file writer for the aligned FASTA file format.

fmt: Optional[str] = 'FASTA'

format_alignment(alignment)

Return a string with the alignment in aligned FASTA format.

__abstractmethods__ = frozenset({})

__annotations__ = {'fmt': 'Optional[str]'}

class Bio.Align.fasta.AlignmentIterator(source)

Bases: Bio.Align.interfaces.AlignmentIterator

Alignment iterator for aligned FASTA files.

An aligned FASTA file contains one multiple alignment. Alignment gaps are represented by dashes in the sequence lines. Header lines start with ‘>’ followed by the name of the sequence, and optionally a description.

fmt: Optional[str] = 'FASTA'

__abstractmethods__ = frozenset({})

__annotations__ = {'fmt': 'Optional[str]'}