bx.align package

Subpackages

• bx.align.sitemask package
  • Submodules
    • bx.align.sitemask.core module
    • bx.align.sitemask.cpg module
    • bx.align.sitemask.quality module
    • bx.align.sitemask.sitemask_tests module
  • Module contents
    • MaskPipeline
    • Masker
• bx.align.tools package
  • Submodules
    • bx.align.tools.chop module
    • bx.align.tools.fuse module
    • bx.align.tools.thread module
    • bx.align.tools.tile module
  • Module contents
    • FusingAlignmentWriter
    • chop_list()
    • fuse()
    • fuse_list()
    • get_components_for_species()
    • intervals_from_mask()
    • tile_interval()

Submodules

• bx.align.axt module
  • Indexed
    • Indexed.get()
    • Indexed.get_axt_at_offset()
  • MultiIndexed
    • MultiIndexed.get()
  • Reader
    • Reader.close()
  • ReaderIter
  • Writer
    • Writer.close()
    • Writer.write()
  • read_next_axt()
  • readline()
• 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
  • Chain
    • Chain.bedInterval()
    • Chain.slice()
  • EPOitem
    • EPOitem.cigar_iter()
    • EPOitem.cigar_pattern
    • EPOitem.intervals()
• bx.align.epo_tests module
  • TestBed
    • TestBed.setUp()
    • TestBed.test_ci()
    • TestBed.test_elem_u()
  • TestEpo
    • TestEpo.setUp()
    • TestEpo.test_make_chain()
    • TestEpo.test_out()
    • TestEpo.test_rem_dash()
  • toCigar()
• bx.align.lav module
  • LavAsPiecesReader
    • LavAsPiecesReader.build_alignment()
  • 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
    • Writer.close()
    • Writer.write()
    • Writer.write_a_stanza()
    • Writer.write_h_stanza()
    • Writer.write_lav_marker()
    • Writer.write_s_stanza()
    • Writer.write_trailer()
  • build_filename()
  • chrom_key()
  • do_path_subs()
  • minus_or_nothing()
  • rc_or_nothing()
  • sort_keys_by_chrom()
• bx.align.lav_tests module
  • check_component()
  • lavTestCase
    • lavTestCase.testReader()
• bx.align.maf module
  • Indexed
  • MAFIndexedAccess
    • MAFIndexedAccess.open_data()
    • MAFIndexedAccess.read_at_current_offset()
  • MAFMultiIndexedAccess
    • MAFMultiIndexedAccess.indexed_access_class
  • MultiIndexed
  • Reader
    • Reader.close()
  • ReaderIter
  • Writer
    • Writer.close()
    • Writer.write()
  • format_tabular()
  • from_string()
  • parse_attributes()
  • read_next_maf()
  • readline()
• bx.align.maf_tests module
  • check_component()
  • test_column_iter()
  • test_read_with_synteny()
  • test_reader()
  • test_remove_all_gap_column()
  • test_reverse_complement()
  • test_slice()
  • test_write_with_synteny()
  • test_writer()
• bx.align.score module
  • ScoringScheme
    • ScoringScheme.score_alignment()
    • ScoringScheme.score_texts()
    • ScoringScheme.set_score()
  • accumulate_scores()
  • build_scoring_scheme()
  • int_or_float()
  • read_scoring_scheme()
  • score_alignment()
  • score_texts()
  • sym_to_char()
• bx.align.score_tests module
  • BasicTests
    • BasicTests.test_accumulate()
    • BasicTests.test_align()
    • BasicTests.test_asymm_scoring()
    • BasicTests.test_nonsymm_scoring()
    • BasicTests.test_scoring_text()

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.