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.EmbossWriter(handle)

Bases: Bio.AlignIO.Interfaces.SequentialAlignmentWriter

Emboss alignment writer (WORK IN PROGRESS).

Writes a simplfied version of the EMBOSS pairs/simple file format. A lot of the information their tools record in their headers is not available and is omitted.


Write header for the file.

Write footer for the file.

write_alignment(self, alignment)

Use this to write (another) single alignment to an open file.

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

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.


Parse the next alignment from the handle.