bx.align.maf module

Support for the MAF multiple sequence alignment format used by multiz.

bx.align.maf.Indexed

Deprecated: MAFIndexedAccess is also available under the name Indexed.

class bx.align.maf.MAFIndexedAccess(data_filename, index_filename=None, keep_open=False, use_cache=False, **kwargs)

Bases: AbstractIndexedAccess

Indexed access to a MAF file.

open_data()

read_at_current_offset(file, **kwargs)

Read the MAF block at the current position in file and return an instance of Alignment.

class bx.align.maf.MAFMultiIndexedAccess(filenames, index_filenames=None, keep_open=False, use_cache=False, **kwargs)

Bases: AbstractMultiIndexedAccess

Indexed access to multiple MAF files.

indexed_access_class

alias of MAFIndexedAccess

bx.align.maf.MultiIndexed

Deprecated: MAFMultiIndexedAccess is also available under the name MultiIndexed.

class bx.align.maf.Reader(file, **kwargs)

Bases: object

Iterate over all maf blocks in a file in order

close()

class bx.align.maf.ReaderIter(reader)

Bases: object

Adapts a Reader to the iterator protocol.

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

Bases: object

close()

write(alignment)

bx.align.maf.format_tabular(rows, align=None)

bx.align.maf.from_string(string, **kwargs)

bx.align.maf.parse_attributes(fields)

Parse list of key=value strings into a dict

bx.align.maf.read_next_maf(file, species_to_lengths=None, parse_e_rows=False)

Read the next MAF block from file and return as an Alignment instance. If parse_e_rows is true, empty components will be created when e rows are encountered.

bx.align.maf.readline(file, skip_blank=False)

Read a line from provided file, skipping any blank or comment lines