Bio.AlignIO.EmbossIO module

Bio.AlignIO support for “emboss” alignment output from EMBOSS tools.

You are expected to use this module via the Bio.AlignIO functions (or the Bio.SeqIO functions if you want to work directly with the gapped sequences).

This module contains a parser for the EMBOSS pairs/simple file format, for example from the alignret, water and needle tools.

class Bio.AlignIO.EmbossIO.EmbossIterator(handle, seq_count=None)

Bases: Bio.AlignIO.Interfaces.AlignmentIterator

Emboss alignment iterator.

For reading the (pairwise) alignments from EMBOSS tools in what they call the “pairs” and “simple” formats.

__next__(self)

Parse the next alignment from the handle.