Bio.Align.bigbed module

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

The bigBed format stores a series of pairwise alignments in a single indexed binary file. Typically they are used for transcript to genome alignments. As in the BED format, the alignment positions and alignment scores are stored, but the aligned sequences are not.

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

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

class Bio.Align.bigbed.Field(type, name, comment)

Bases: tuple

__getnewargs__()

Return self as a plain tuple. Used by copy and pickle.

static __new__(_cls, type, name, comment)

Create new instance of Field(type, name, comment)

__repr__()

Return a nicely formatted representation string

__slots__ = ()

comment

Alias for field number 2

name

Alias for field number 1

type

Alias for field number 0

class Bio.Align.bigbed.AutoSQLTable(text=None)

Bases: object

AutoSQL table describing the columns of an (possibly extended) BED format.

__init__(text=None)

Create an AutoSQL table describing the columns of an (extended) BED format.

__str__()

Return str(self).

class Bio.Align.bigbed.AlignmentIterator(source)

Bases: Bio.Align.interfaces.AlignmentIterator

Alignment iterator for bigBed files.

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

__init__(source)

Create an AlignmentIterator object.

Arguments:

• source - input data or file name

__abstractmethods__ = frozenset({})

__len__()

search(chromosome=None, start=None, end=None)

Iterate over alignments overlapping the specified chromosome region..

This method searches the index to find alignments to the specified chromosome that fully or partially overlap the chromosome region between start and end.

Arguments:

• chromosome - chromosome name. If None (default value), include all alignments.

• start - starting position on the chromosome. If None (default value), use 0 as the starting position.

• end - end position on the chromosome. If None (default value), use the length of the chromosome as the end position.