Bio.Align.a2m module

Bio.Align support for A2M files.

A2M files are alignment files created by align2model or hmmscore in the SAM Sequence Alignment and Modeling Software System.

class Bio.Align.a2m.AlignmentWriter(target)

Bases: Bio.Align.interfaces.AlignmentWriter

Alignment file writer for the A2M file format.

__init__(target)

Create an AlignmentWriter object.

Arguments:

• target - output stream or file name

format_alignment(alignment)

Return a string with the alignment in the A2M file format.

class Bio.Align.a2m.AlignmentIterator(source)

Bases: Bio.Align.interfaces.AlignmentIterator

Alignment iterator for files in the A2M file format.

An A2M file contains one multiple alignment. Matches are represented by upper case letters and deletions by dashes in alignment columns containing matches or deletions only. Insertions are represented by lower case letters, with gaps aligned to the insertion shown as periods. Header lines start with ‘>’ followed by the name of the sequence, and optionally a description.

__init__(source)

Create an AlignmentIterator object.

Arguments:

• source - input data or file name

__abstractmethods__ = frozenset({})