bx.align package
Subpackages
Submodules
- bx.align.axt module
- bx.align.core module
Alignment
Alignment.add_component()
Alignment.column_iter()
Alignment.get_component_by_src()
Alignment.get_component_by_src_start()
Alignment.get_components_by_src()
Alignment.get_score()
Alignment.limit_to_species()
Alignment.remove_all_gap_columns()
Alignment.reverse_complement()
Alignment.score
Alignment.set_score()
Alignment.slice()
Alignment.slice_by_component()
Alignment.src_size()
Component
Component.coord_to_col()
Component.end
Component.forward_strand_end
Component.forward_strand_start
Component.get_end()
Component.get_forward_strand_end()
Component.get_forward_strand_start()
Component.get_src_size()
Component.reverse_complement()
Component.set_src_size()
Component.slice()
Component.slice_by_coord()
Component.src_size
get_indexed()
get_reader()
get_writer()
shuffle_columns()
src_merge()
src_split()
- bx.align.epo module
- bx.align.epo_tests module
- bx.align.lav module
LavAsPiecesReader
Reader
Reader.build_alignment()
Reader.close()
Reader.close_seqs()
Reader.d_stanza()
Reader.fetch_line()
Reader.h_stanza()
Reader.header_to_src_name()
Reader.open_seqs()
Reader.parse_a_stanza()
Reader.parse_h_stanza()
Reader.parse_s_seq()
Reader.parse_s_stanza()
Reader.parse_unknown_stanza()
Reader.path_to_src_name()
Reader.s_stanza()
ReaderIter
Writer
build_filename()
chrom_key()
do_path_subs()
minus_or_nothing()
rc_or_nothing()
sort_keys_by_chrom()
- bx.align.lav_tests module
- bx.align.maf module
- bx.align.maf_tests module
- bx.align.score module
- bx.align.score_tests module
Module contents
Support for dealing with (genome scale) sequence alignments. See core for the abstract alignment classes and maf, axt, and lav for readers and writers in various formats.