bx.align.core module

Classes that represent alignments between multiple sequences.

class bx.align.core.Alignment(score=0, attributes=None, species_to_lengths=None)

Bases: object

add_component(component)

column_iter()

get_component_by_src(src)

get_component_by_src_start(src)

get_components_by_src(src)

get_score()

limit_to_species(species)

remove_all_gap_columns()

Remove any columns containing only gaps from alignment components, text of components is modified IN PLACE.

reverse_complement()

property score

set_score(score)

slice(start, end)

slice_by_component(component_index, start, end)

Return a slice of the alignment, corresponding to an coordinate interval in a specific component.

component_index is one of

an integer offset into the components list a string indicating the src of the desired component a component

start and end are relative to the + strand, regardless of the component’s strand.

src_size(src)

class bx.align.core.Component(src='', start=0, size=0, strand=None, src_size=None, text='')

Bases: object

coord_to_col(pos)

Return the alignment column index corresponding to coordinate pos.

pos is relative to the + strand, regardless of the component’s strand.

property end

property forward_strand_end

property forward_strand_start

get_end()

get_forward_strand_end()

get_forward_strand_start()

get_src_size()

reverse_complement()

set_src_size(src_size)

slice(start, end)

slice_by_coord(start, end)

Return the slice of the component corresponding to a coordinate interval.

start and end are relative to the + strand, regardless of the component’s strand.

property src_size

bx.align.core.get_indexed(format, filename, index_filename=None, keep_open=False, species_to_lengths=None)

bx.align.core.get_reader(format, infile, species_to_lengths=None)

bx.align.core.get_writer(format, outfile, attributes=None)

bx.align.core.shuffle_columns(a)

Randomize the columns of an alignment

bx.align.core.src_merge(species, chrom, contig=None)

bx.align.core.src_split(src)