Bio.Align.bigpsl module

Bio.Align support for alignment files in the bigPsl format.

A bigPsl file is a bigBed file with a BED12+13 format consisting of the 12 predefined BED fields and 13 custom fields defined in the autoSql file bigPsl.as. This module uses the Bio.Align.bigbed module to parse the file, but stores the data in a PSL-consistent manner as defined in bigPsl.as. As the bigPsl format is a special case of the bigBed format, bigPsl files are binary and are indexed as bigBed files.

See http://genome.ucsc.edu/goldenPath/help/bigPsl.html for more information.

You are expected to use this module via the Bio.Align functions.

class Bio.Align.bigpsl.AlignmentIterator(source)

Bases: Bio.Align.bigbed.AlignmentIterator

Alignment iterator for bigPsl files.

The pairwise alignments stored in the bigPsl file are loaded and returned incrementally. Additional alignment information is stored as attributes of each alignment.

__abstractmethods__ = frozenset({})