bx.align.axt module

Support for reading and writing the AXT format used for pairwise alignments.

class bx.align.axt.Indexed(axt_filename, index_filename=None, keep_open=False, species1=None, species2=None, species_to_lengths=None, support_ids=False)

Bases: object

Indexed access to a axt using overlap queries, requires an index file

get(src, start, end)

get_axt_at_offset(offset)

class bx.align.axt.MultiIndexed(axt_filenames, keep_open=False)

Bases: object

Similar to ‘indexed’ but wraps more than one axt_file

get(src, start, end)

class bx.align.axt.Reader(file, species1=None, species2=None, species_to_lengths=None, support_ids=False)

Bases: object

Iterate over all axt blocks in a file in order

close()

class bx.align.axt.ReaderIter(reader): Bases: object

class bx.align.axt.Writer(file, attributes=None)

Bases: object

close()

write(alignment)

bx.align.axt.read_next_axt(file, species1, species2, species_to_lengths=None, support_ids=False)

bx.align.axt.readline(file, skip_blank=False): Read a line from provided file, skipping any blank or comment lines