Bio.SeqIO.GfaIO module

Bio.SeqIO support for the Graphical Fragment Assembly format.

This format is output by many assemblers and includes linkage information for how the different sequences fit together, however, we just care about the segment (sequence) information.

Documentation: - Version 1.x: https://gfa-spec.github.io/GFA-spec/GFA1.html - Version 2.0: https://gfa-spec.github.io/GFA-spec/GFA2.html

class Bio.SeqIO.GfaIO.Gfa1Iterator(source: IO[str] | PathLike | str | bytes)

Bases: SequenceIterator

Parser for GFA 1.x files.

Documentation: https://gfa-spec.github.io/GFA-spec/GFA1.html

modes = 't'

__init__(source: IO[str] | PathLike | str | bytes) → None

Iterate over a GFA file as SeqRecord objects.

Arguments:

source - input stream opened in text mode, or a path to a file

__next__()

Return the next SeqRecord.

This method must be implemented by the subclass.

__abstractmethods__ = frozenset({})

__parameters__ = ()

class Bio.SeqIO.GfaIO.Gfa2Iterator(source: IO[str] | PathLike | str | bytes)