Index

A

AbstractTests (class in bx.bitset_tests) abut() (in module bx_extras.pstat) accumulate_scores() (in module bx.align.score) actions (bx.motif.io.transfac.TransfacWriter attribute) add() (bx.interval_index_file.Index method) (bx.interval_index_file.Indexes method) (bx.intervals.intersection.IntervalTree method) (bx.intervals.IntervalTree method) add_component() (bx.align.core.Alignment method) add_interval() (bx.intervals.intersection.IntervalTree method) (bx.intervals.IntervalTree method) after() (bx.intervals.intersection.IntervalTree method) (bx.intervals.IntervalTree method) after_interval() (bx.intervals.intersection.IntervalTree method) (bx.intervals.IntervalTree method)

Align (class in bx.pwm.position_weight_matrix) Alignment (class in bx.align.core) alignment_mapping_from_file() (in module bx.seqmapping) AlignmentMappingTests (class in bx.seqmapping_tests) AlignScoreMatrix (class in bx.pwm.position_weight_matrix) append() (bx.filter.Pipeline method) array_tree_dict_from_reader() (in module bx.arrays.array_tree) ArrayAccumulatingBlockHandler (class in bx.bbi.bigwig_file) ArrayTree (class in bx.arrays.array_tree) as_dict() (bx.motif.io.transfac.TransfacReader method) assert_bits() (bx.bitset_tests.AbstractTests method) attach() (bx.bbi.bpt_file.BPTFile method) (bx.bbi.cirtree_file.CIRTreeFile method) attribute() (in module bx.cookbook.attribute)

B

bad_sect() (in module bx.intervals.operations.quicksect) BadMagicNumber base_coverage() (in module bx.intervals.operations.base_coverage) BaseMatrix (class in bx.motif.pwm) BasicTests (class in bx.align.score_tests) BBIFile (class in bx.bbi.bbi_file) bedInterval() (bx.align.epo.Chain method) BedReader (class in bx.arrays.bed) before() (bx.intervals.intersection.IntervalTree method) (bx.intervals.IntervalTree method) before_interval() (bx.intervals.intersection.IntervalTree method) (bx.intervals.IntervalTree method) BGZFFile (class in bx.misc.bgzf) BigBedBlockHandler (class in bx.bbi.bigbed_file) BigBedFile (class in bx.bbi.bigbed_file) BigWigBlockHandler (class in bx.bbi.bigwig_file) BigWigFile (class in bx.bbi.bigwig_file) BigWigHeaderBlockHandler (class in bx.bbi.bigwig_file) bin_size (bx.bitset.BinnedBitSet attribute) BinaryFileReader (class in bx.misc.binary_file) BinaryFileWriter (class in bx.misc.binary_file) binned_bitsets() (bx.intervals.io.GenomicIntervalReader method) binned_bitsets_by_chrom() (in module bx.bitset_builders) binned_bitsets_from_bed_file() (in module bx.bitset_builders) binned_bitsets_from_file() (in module bx.bitset_builders) binned_bitsets_from_list() (in module bx.bitset_builders) binned_bitsets_proximity() (in module bx.bitset_builders) BinnedArray (class in bx.binned_array) BinnedArrayWriter (class in bx.binned_array) BinnedBitSet (class in bx.bitset) BinnedBitSetTests (class in bx.bitset_tests) bits2list() (in module bx.bitset_utils) bits_clear_in_range() (in module bx.intervals.operations) bits_set_in_range() (in module bx.intervals.operations) BitSet (class in bx.bitset) bitset_complement() (in module bx.bitset_utils) bitset_intersect() (in module bx.bitset_utils) bitset_interval_intersect() (in module bx.bitset_utils) bitset_subtract() (in module bx.bitset_utils) bitset_union() (in module bx.bitset_utils) BitsetSafeReaderWrapper (class in bx.intervals.io) BitSetTests (class in bx.bitset_tests) block_size (bx.arrays.array_tree.ArrayTree attribute) BlockHandler (class in bx.bbi.bbi_file) BPTFile (class in bx.bbi.bpt_file) build_alignment() (bx.align.lav.LavAsPiecesReader method) (bx.align.lav.Reader method) build_filename() (in module bx.align.lav) build_scoring_scheme() (in module bx.align.score) bx module bx.align module bx.align.axt module bx.align.core module bx.align.epo module bx.align.epo_tests module bx.align.lav module bx.align.lav_tests module bx.align.maf module bx.align.maf_tests module bx.align.score module bx.align.score_tests module bx.align.sitemask module bx.align.sitemask.core module bx.align.sitemask.cpg module bx.align.sitemask.quality module bx.align.sitemask.sitemask_tests module bx.align.tools module bx.align.tools.chop module bx.align.tools.fuse module bx.align.tools.thread module bx.align.tools.tile module bx.arrays module bx.arrays.array_tree module bx.arrays.array_tree_tests module bx.arrays.bed module bx.arrays.wiggle module bx.bbi module bx.bbi.bbi_file module bx.bbi.bigbed_file module bx.bbi.bigwig_file module bx.bbi.bpt_file module bx.bbi.cirtree_file module bx.binned_array module bx.bitset module bx.bitset_builders module bx.bitset_tests module bx.bitset_utils module bx.cookbook module bx.cookbook.attribute module bx.cookbook.doc_optparse module bx.filter module bx.gene_reader module bx.interval_index_file module bx.interval_index_file_tests module bx.intervals module bx.intervals.cluster module bx.intervals.cluster_tests module bx.intervals.intersection module

bx.intervals.intersection_tests module bx.intervals.io module bx.intervals.operations module bx.intervals.operations.base_coverage module bx.intervals.operations.complement module bx.intervals.operations.concat module bx.intervals.operations.coverage module bx.intervals.operations.find_clusters module bx.intervals.operations.intersect module bx.intervals.operations.join module bx.intervals.operations.merge module bx.intervals.operations.quicksect module bx.intervals.operations.subtract module bx.intervals.random_intervals module bx.intseq module bx.intseq.ngramcount module bx.misc module bx.misc.bgzf module bx.misc.bgzf_tests module bx.misc.binary_file module bx.misc.cdb module bx.misc.cdb_tests module bx.misc.filecache module bx.misc.filecache_tests module bx.misc.readlengths module bx.misc.seekbzip2 module bx.misc.seekbzip2_tests module bx.misc.seeklzop module bx.misc.seeklzop_tests module bx.motif module bx.motif.io module bx.motif.io.transfac module bx.motif.io.transfac_tests module bx.motif.logo module bx.motif.pwm module bx.motif.pwm_tests module bx.phylo module bx.phylo.newick module bx.phylo.phast module bx.phylo.phast_tests module bx.pwm module bx.pwm.bed_score_aligned_pwm module bx.pwm.bed_score_aligned_string module bx.pwm.maf_select_motifs module bx.pwm.position_weight_matrix module bx.pwm.pwm_score_maf module bx.pwm.pwm_score_motifs module bx.pwm.pwm_score_positions module bx.pwm.pwm_tests module bx.seq module bx.seq.core module bx.seq.fasta module bx.seq.fasta_tests module bx.seq.nib module bx.seq.nib_tests module bx.seq.qdna module bx.seq.qdna_tests module bx.seq.seq module bx.seq.seq_tests module bx.seq.twobit module bx.seqmapping module bx.seqmapping_tests module bx.tabular module bx.tabular.io module bx.wiggle module bx.wiggle_tests module bx_extras module bx_extras.fpconst module bx_extras.lrucache module bx_extras.pstat module bx_extras.stats module bytes_required() (bx.interval_index_file.Index method) bytesify() (in module bx.binned_array) (in module bx.misc.binary_file)

C

cachedmethod() (in module bx.cookbook) CacheKeyError cdbhash() (in module bx.misc.cdb) CDSReader() (in module bx.gene_reader) Chain (class in bx.align.epo) CharMappingTests (class in bx.seqmapping_tests) check_component() (in module bx.align.lav_tests) (in module bx.align.maf_tests) check_get() (in module bx.seq.fasta_tests) (in module bx.seq.nib_tests) (in module bx.seq.qdna_tests) (in module bx.seq.seq_tests) chop_list() (in module bx.align.tools) (in module bx.align.tools.chop) chrom (bx.intervals.intersection.Interval attribute) (bx.intervals.Interval attribute) chrom_id (bx.bbi.bbi_file.SummaryBlock attribute) chrom_key() (in module bx.align.lav) cigar_iter() (bx.align.epo.EPOitem method) cigar_pattern (bx.align.epo.EPOitem attribute) CIRTreeFile (class in bx.bbi.cirtree_file) clear() (bx.bitset.BinnedBitSet method) (bx.bitset.BitSet method) (bx.cookbook.ImmutableDict method) clone() (bx.bitset.BitSet method) close() (bx.align.axt.Reader method) (bx.align.axt.Writer method) (bx.align.lav.Reader method) (bx.align.lav.Writer method) (bx.align.maf.Reader method) (bx.align.maf.Writer method) (bx.align.tools.fuse.FusingAlignmentWriter method) (bx.align.tools.FusingAlignmentWriter method) (bx.misc.bgzf.BGZFFile method) (bx.misc.filecache.FileCache method) (bx.misc.seekbzip2.SeekableBzip2File method) (bx.misc.seeklzop.SeekableLzopFile method) (bx.pwm.position_weight_matrix.Reader method) (bx.seq.fasta.FastaWriter method) (bx.seq.nib.NibWriter method) (bx.seq.qdna.QdnaWriter method) (bx.seq.seq.SeqFile method) (bx.seq.seq.SeqReader method)

close_seqs() (bx.align.lav.Reader method) ClusterNode (class in bx.intervals.operations.find_clusters) ClusterTree (class in bx.intervals.cluster) cmp() (in module bx_extras.pstat) colex() (in module bx_extras.pstat) collapse() (in module bx_extras.pstat) column_iter() (bx.align.core.Alignment method) Comment (class in bx.tabular.io) complement() (in module bx.intervals.operations.complement) complementMap (bx.pwm.position_weight_matrix.PositionWeightMatrix attribute) Component (class in bx.align.core) concat() (in module bx.intervals.operations.concat) consensus_symbol() (in module bx.pwm.position_weight_matrix) coord_to_col() (bx.align.core.Component method) copy() (bx.intervals.io.GenomicInterval method) corrected_probability_score() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) correlation() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) count_ngrams() (in module bx.intseq.ngramcount) count_range() (bx.bitset.BinnedBitSet method) (bx.bitset.BitSet method) coverage() (in module bx.intervals.operations.coverage) create_from_other() (bx.motif.pwm.BaseMatrix class method) cross_lists() (in module bx.cookbook)

D

d_stanza() (bx.align.lav.Reader method) data_offset (bx.bbi.bbi_file.ZoomLevel attribute) DEFAULT_CORRECTION (bx.motif.pwm.FrequencyMatrix attribute) DEFAULT_SIZE (in module bx_extras.lrucache) dict_to_file() (bx.arrays.array_tree.FileArrayTreeDict class method) Dispatch (class in bx_extras.stats)

dm() (in module bx_extras.pstat) do_path_subs() (in module bx.align.lav) downstream_of_interval() (bx.intervals.intersection.IntervalTree method) (bx.intervals.IntervalTree method) dtype (bx.arrays.array_tree.ArrayTree attribute) duplicates() (in module bx_extras.pstat)

E

Edge (class in bx.phylo.newick) end (bx.align.core.Component property) (bx.bbi.bbi_file.SummarizedData attribute) (bx.bbi.bbi_file.SummaryBlock attribute) (bx.intervals.intersection.Interval attribute) (bx.intervals.intersection.IntervalNode attribute) (bx.intervals.Interval attribute) (bx.intervals.IntervalNode attribute)

EPOitem (class in bx.align.epo) eps_logo() (in module bx.motif.logo) exception() (in module bx.cookbook.doc_optparse) exit() (in module bx.cookbook.doc_optparse) extend() (bx.filter.Pipeline method) extract_name() (bx.seq.seq.SeqFile method)

F

FastaFile (class in bx.seq.fasta) FastaReader (class in bx.seq.fasta) FASTATestCase (class in bx.seq.fasta_tests) FastaWriter (class in bx.seq.fasta) FeatureReader() (in module bx.gene_reader) fetch_line() (bx.align.lav.Reader method) FieldFormatError fieldnames (bx.tabular.io.TableRow property) FileArrayTreeDict (class in bx.arrays.array_tree) FileBinnedArray (class in bx.binned_array) FileCache (class in bx.misc.filecache) FileCDBDict (class in bx.misc.cdb) Filter (class in bx.filter) find() (bx.bbi.bpt_file.BPTFile method) (bx.interval_index_file.Index method) (bx.interval_index_file.Indexes method) (bx.intervals.intersection.IntervalNode method) (bx.intervals.intersection.IntervalTree method) (bx.intervals.IntervalNode method) (bx.intervals.IntervalTree method) find_clusters() (in module bx.intervals.operations.find_clusters) find_overlapping_blocks() (bx.bbi.cirtree_file.CIRTreeFile method) findintersect() (in module bx.intervals.operations.join) findoverlap() (in module bx.intervals.operations.join) finish() (bx.binned_array.BinnedArrayWriter method)

fix_dirty() (bx.misc.filecache.FileCache method) (bx.misc.seekbzip2.SeekableBzip2File method) (bx.misc.seeklzop.SeekableLzopFile method) flat() (in module bx_extras.pstat) flatten() (in module bx.cookbook) flush() (bx.binned_array.BinnedArrayWriter method) (bx.misc.seekbzip2.SeekableBzip2File method) (bx.misc.seeklzop.SeekableLzopFile method) format_tabular() (in module bx.align.maf) (in module bx.pwm.maf_select_motifs) forward_strand_end (bx.align.core.Component property) forward_strand_start (bx.align.core.Component property) freqs_to_heights() (in module bx.motif.logo) FrequencyMatrix (class in bx.motif.pwm) from_file() (bx.arrays.array_tree.ArrayTree class method) (bx.phylo.phast.TreeModel static method) from_rows() (bx.motif.pwm.BaseMatrix class method) from_sequence() (bx.arrays.array_tree.ArrayTree class method) from_string() (in module bx.align.maf) fuse() (in module bx.align.tools) (in module bx.align.tools.fuse) fuse_list() (in module bx.align.tools) (in module bx.align.tools.fuse) FusingAlignmentWriter (class in bx.align.tools) (class in bx.align.tools.fuse)

G

GeneReader() (in module bx.gene_reader) GenomicInterval (class in bx.intervals.io) GenomicIntervalReader (class in bx.intervals.io) get() (bx.align.axt.Indexed method) (bx.align.axt.MultiIndexed method) (bx.bbi.bigbed_file.BigBedFile method) (bx.bbi.bigwig_file.BigWigFile method) (bx.binned_array.BinnedArray method) (bx.binned_array.FileBinnedArray method) (bx.bitset.BitSet method) (bx.interval_index_file.Indexes method) (bx.misc.seeklzop.UnpackWrapper method) (bx.seq.seq.SeqFile method) (bx.seq.twobit.TwoBitSequence method) get_as_array() (bx.bbi.bigwig_file.BigWigFile method) get_axt_at_offset() (bx.align.axt.Indexed method) get_bin_offset() (bx.binned_array.BinnedArray method) (bx.binned_array.FileBinnedArray method) get_block_and_offset() (bx.misc.filecache.FileCache method) (bx.misc.seeklzop.SeekableLzopFile method) get_chunk_and_offset() (bx.misc.seekbzip2.SeekableBzip2File method) get_component_by_src() (bx.align.core.Alignment method) get_component_by_src_start() (bx.align.core.Alignment method)

get_components_by_src() (bx.align.core.Alignment method) get_components_for_species() (in module bx.align.tools) (in module bx.align.tools.thread) get_ctcf_rows() (in module bx.motif.pwm_tests) get_end() (bx.align.core.Component method) get_forward_strand_end() (bx.align.core.Component method) get_forward_strand_start() (bx.align.core.Component method) get_headers() (bx.bbi.bigwig_file.BigWigFile method) get_indexed() (in module bx.align.core) get_masked() (bx.align.sitemask.core.MaskPipeline method) (bx.align.sitemask.MaskPipeline method) get_quantum() (bx.seq.qdna.QdnaFile method) get_range() (bx.binned_array.BinnedArray method) (bx.binned_array.FileBinnedArray method) get_reader() (in module bx.align.core) get_score() (bx.align.core.Alignment method) get_src_size() (bx.align.core.Component method) get_value_size() (bx.interval_index_file.Index method) get_writer() (in module bx.align.core) getintervals() (bx.intervals.operations.find_clusters.ClusterNode method) getlines() (bx.intervals.cluster.ClusterTree method) (bx.intervals.operations.find_clusters.ClusterNode method) getregions() (bx.intervals.cluster.ClusterTree method)

H

h_stanza() (bx.align.lav.Reader method) Header (class in bx.tabular.io)

header_to_src_name() (bx.align.lav.Reader method) help_callback() (in module bx.cookbook.doc_optparse)

I

iand() (bx.bitset.BinnedBitSet method) (bx.bitset.BitSet method) identity_mapping() (in module bx.seqmapping) ImmutableDict (class in bx.cookbook) Inclusive (class in bx.align.sitemask.cpg) Index (class in bx.interval_index_file) index_offset (bx.bbi.bbi_file.ZoomLevel attribute) Indexed (class in bx.align.axt) (in module bx.align.maf) indexed_access_class (bx.align.maf.MAFMultiIndexedAccess attribute) Indexes (class in bx.interval_index_file) infer_format() (in module bx.seq) (in module bx.seq.core) information_base_content() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) information_content_calculation() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) init_bin() (bx.binned_array.BinnedArray method) init_bz2() (bx.misc.seekbzip2.SeekableBzip2File method) init_table() (bx.misc.seekbzip2.SeekableBzip2File method) (bx.misc.seeklzop.SeekableLzopFile method) insert() (bx.intervals.cluster.ClusterTree method) (bx.intervals.intersection.IntervalNode method) (bx.intervals.intersection.IntervalTree method) (bx.intervals.IntervalNode method) (bx.intervals.IntervalTree method) (bx.intervals.operations.find_clusters.ClusterNode method) (bx.intervals.operations.quicksect.IntervalNode method) (bx.intervals.operations.quicksect.IntervalTree method) insert_interval() (bx.intervals.intersection.IntervalTree method) (bx.intervals.IntervalTree method) insertpairs() (bx.intervals.cluster_tests.TestCluster method) int_or_float() (in module bx.align.score) intersect() (bx.intervals.intersection.IntervalNode method) (bx.intervals.IntervalNode method) (bx.intervals.operations.quicksect.IntervalNode method) (bx.intervals.operations.quicksect.IntervalTree method) (in module bx.intervals.operations.intersect) Intersecter (in module bx.intervals) (in module bx.intervals.intersection)

interval (bx.intervals.intersection.IntervalNode attribute) (bx.intervals.IntervalNode attribute) Interval (class in bx.intervals) (class in bx.intervals.intersection) interval_cmp() (in module bx.intervals.operations.join) IntervalAccumulatingBlockHandler (class in bx.bbi.bigbed_file) (class in bx.bbi.bigwig_file) IntervalNode (class in bx.intervals) (class in bx.intervals.intersection) (class in bx.intervals.operations.quicksect) IntervalReader() (in module bx.wiggle) intervals() (bx.align.epo.EPOitem method) intervals_from_mask() (in module bx.align.tools) (in module bx.align.tools.tile) IntervalTree (class in bx.intervals) (class in bx.intervals.intersection) (class in bx.intervals.operations.quicksect) IntervalTreeTest (class in bx.intervals.intersection_tests) IntMappingTests (class in bx.seqmapping_tests) invert() (bx.bitset.BinnedBitSet method) (bx.bitset.BitSet method) ior() (bx.bitset.BinnedBitSet method) (bx.bitset.BitSet method) isFinite() (in module bx_extras.fpconst) isInf() (in module bx_extras.fpconst) isnan() (in module bx.pwm.bed_score_aligned_pwm) (in module bx.pwm.bed_score_aligned_string) (in module bx.pwm.maf_select_motifs) (in module bx.pwm.position_weight_matrix) (in module bx.pwm.pwm_score_maf) (in module bx.pwm.pwm_score_motifs) (in module bx.pwm.pwm_score_positions) isNaN() (in module bx_extras.fpconst) isNegInf() (in module bx_extras.fpconst) isPosInf() (in module bx_extras.fpconst) iterate() (bx.interval_index_file.Index method) iterwrapper() (bx.intervals.io.NiceReaderWrapper method) ixor() (bx.bitset.BitSet method)

J

join() (in module bx.intervals.operations.join)

L

LavAsPiecesReader (class in bx.align.lav) lavTestCase (class in bx.align.lav_tests) lbetacf() (in module bx_extras.stats) lbetai() (in module bx_extras.stats) lchisqprob() (in module bx_extras.stats) lchisquare() (in module bx_extras.stats) lcumfreq() (in module bx_extras.stats) lcumsum() (in module bx_extras.stats) ldescribe() (in module bx_extras.stats) left() (bx.intervals.intersection.IntervalNode method) (bx.intervals.IntervalNode method) left_node (bx.intervals.intersection.IntervalNode attribute) (bx.intervals.IntervalNode attribute) lerfcc() (in module bx_extras.stats) level_list (bx.bbi.bbi_file.BBIFile attribute) levels (bx.arrays.array_tree.ArrayTree attribute) lF_oneway() (in module bx_extras.stats) lF_value() (in module bx_extras.stats) lfindwithin() (in module bx_extras.stats) lfprob() (in module bx_extras.stats) lfriedmanchisquare() (in module bx_extras.stats) lgammln() (in module bx_extras.stats) lgeometricmean() (in module bx_extras.stats) lharmonicmean() (in module bx_extras.stats) lhistogram() (in module bx_extras.stats) limit_to_species() (bx.align.core.Alignment method) lincr() (in module bx_extras.stats) linedelimited() (in module bx_extras.pstat) lineincols() (in module bx_extras.pstat) lineincustcols() (in module bx_extras.pstat) linexand() (in module bx_extras.pstat) linexor() (in module bx_extras.pstat) list2bits() (in module bx.bitset_utils) list2string() (in module bx_extras.pstat) litemfreq() (in module bx_extras.stats) lkendalltau() (in module bx_extras.stats) lkruskalwallish() (in module bx_extras.stats) lks_2samp() (in module bx_extras.stats) lksprob() (in module bx_extras.stats) lkurtosis() (in module bx_extras.stats) llinregress() (in module bx_extras.stats) lmannwhitneyu() (in module bx_extras.stats) lmean() (in module bx_extras.stats) lmedian() (in module bx_extras.stats)

lmedianscore() (in module bx_extras.stats) lmode() (in module bx_extras.stats) lmoment() (in module bx_extras.stats) load_bin() (bx.binned_array.FileBinnedArray method) (bx.interval_index_file.Index method) load_block() (bx.misc.filecache.FileCache method) (bx.misc.seeklzop.SeekableLzopFile method) load_sequence() (bx.seq.twobit.TwoBitFile method) lobrientransform() (in module bx_extras.stats) LotsaTestCase (class in bx.intervals.intersection_tests) lpaired() (in module bx_extras.stats) lpearsonr() (in module bx_extras.stats) lpercentileofscore() (in module bx_extras.stats) lpointbiserialr() (in module bx_extras.stats) lrankdata() (in module bx_extras.stats) lranksums() (in module bx_extras.stats) lrelfreq() (in module bx_extras.stats) LRUCache (class in bx_extras.lrucache) lsamplestdev() (in module bx_extras.stats) lsamplevar() (in module bx_extras.stats) lscoreatpercentile() (in module bx_extras.stats) lsem() (in module bx_extras.stats) lshellsort() (in module bx_extras.stats) lskew() (in module bx_extras.stats) lspearmanr() (in module bx_extras.stats) lsquare_of_sums() (in module bx_extras.stats) lss() (in module bx_extras.stats) lstdev() (in module bx_extras.stats) lsterr() (in module bx_extras.stats) lsum() (in module bx_extras.stats) lsumdiffsquared() (in module bx_extras.stats) lsummult() (in module bx_extras.stats) ltiecorrect() (in module bx_extras.stats) ltrim1() (in module bx_extras.stats) ltrimboth() (in module bx_extras.stats) lttest_1samp() (in module bx_extras.stats) lttest_ind() (in module bx_extras.stats) lttest_rel() (in module bx_extras.stats) lvar() (in module bx_extras.stats) lvariation() (in module bx_extras.stats) lwilcoxont() (in module bx_extras.stats) lz() (in module bx_extras.stats) lzprob() (in module bx_extras.stats) lzs() (in module bx_extras.stats)

M

MafBlockScorer() (in module bx.pwm.pwm_score_maf) MAFIndexedAccess (class in bx.align.maf) MafMotifScorer() (in module bx.pwm.pwm_score_maf) MafMotifSelect() (in module bx.pwm.pwm_score_maf) MAFMultiIndexedAccess (class in bx.align.maf) MafScorer() (in module bx.pwm.pwm_score_maf) mafwrite() (in module bx.pwm.maf_select_motifs) magic (bx.bbi.bbi_file.BBIFile attribute) main() (in module bx.intervals.operations.quicksect) (in module bx.pwm.bed_score_aligned_pwm) (in module bx.pwm.bed_score_aligned_string) (in module bx.pwm.maf_select_motifs) (in module bx.pwm.pwm_score_maf) (in module bx.pwm.pwm_score_motifs) (in module bx.pwm.pwm_score_positions) makelol() (in module bx_extras.pstat) makestr() (in module bx_extras.pstat) mask_columns() (in module bx.align.sitemask.cpg) masked (bx.align.sitemask.core.MaskPipeline property) (bx.align.sitemask.MaskPipeline property) masked_block_sizes (bx.seq.twobit.TwoBitSequence attribute) masked_block_starts (bx.seq.twobit.TwoBitSequence attribute) Masker (class in bx.align.sitemask) (class in bx.align.sitemask.core) MaskPipeline (class in bx.align.sitemask) (class in bx.align.sitemask.core) match_consensus() (in module bx.pwm.position_weight_matrix) max (bx.arrays.array_tree.ArrayTree attribute) max_correlation() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) max_val (bx.bbi.bbi_file.SummarizedData attribute) (bx.bbi.bbi_file.SummaryBlock attribute) MaxtriesException Memoize (class in bx.cookbook) memoized (class in bx.cookbook) merge() (in module bx.intervals.operations.merge) min_val (bx.bbi.bbi_file.SummarizedData attribute) (bx.bbi.bbi_file.SummaryBlock attribute) minus_or_nothing() (in module bx.align.lav) MissingFieldError module bx bx.align bx.align.axt bx.align.core bx.align.epo bx.align.epo_tests bx.align.lav bx.align.lav_tests bx.align.maf bx.align.maf_tests bx.align.score bx.align.score_tests bx.align.sitemask bx.align.sitemask.core bx.align.sitemask.cpg bx.align.sitemask.quality bx.align.sitemask.sitemask_tests bx.align.tools bx.align.tools.chop bx.align.tools.fuse bx.align.tools.thread bx.align.tools.tile bx.arrays bx.arrays.array_tree bx.arrays.array_tree_tests bx.arrays.bed bx.arrays.wiggle bx.bbi bx.bbi.bbi_file bx.bbi.bigbed_file bx.bbi.bigwig_file bx.bbi.bpt_file bx.bbi.cirtree_file bx.binned_array bx.bitset bx.bitset_builders bx.bitset_tests bx.bitset_utils bx.cookbook bx.cookbook.attribute bx.cookbook.doc_optparse bx.filter bx.gene_reader bx.interval_index_file bx.interval_index_file_tests bx.intervals bx.intervals.cluster bx.intervals.cluster_tests bx.intervals.intersection bx.intervals.intersection_tests bx.intervals.io bx.intervals.operations bx.intervals.operations.base_coverage bx.intervals.operations.complement bx.intervals.operations.concat bx.intervals.operations.coverage bx.intervals.operations.find_clusters bx.intervals.operations.intersect bx.intervals.operations.join bx.intervals.operations.merge bx.intervals.operations.quicksect bx.intervals.operations.subtract bx.intervals.random_intervals bx.intseq bx.intseq.ngramcount bx.misc bx.misc.bgzf bx.misc.bgzf_tests bx.misc.binary_file bx.misc.cdb bx.misc.cdb_tests bx.misc.filecache bx.misc.filecache_tests bx.misc.readlengths bx.misc.seekbzip2 bx.misc.seekbzip2_tests bx.misc.seeklzop bx.misc.seeklzop_tests bx.motif bx.motif.io bx.motif.io.transfac bx.motif.io.transfac_tests bx.motif.logo bx.motif.pwm bx.motif.pwm_tests bx.phylo bx.phylo.newick bx.phylo.phast bx.phylo.phast_tests bx.pwm bx.pwm.bed_score_aligned_pwm bx.pwm.bed_score_aligned_string bx.pwm.maf_select_motifs bx.pwm.position_weight_matrix bx.pwm.pwm_score_maf bx.pwm.pwm_score_motifs bx.pwm.pwm_score_positions bx.pwm.pwm_tests bx.seq bx.seq.core bx.seq.fasta bx.seq.fasta_tests bx.seq.nib bx.seq.nib_tests bx.seq.qdna bx.seq.qdna_tests bx.seq.seq bx.seq.seq_tests bx.seq.twobit bx.seqmapping bx.seqmapping_tests bx.tabular bx.tabular.io bx.wiggle bx.wiggle_tests bx_extras bx_extras.fpconst bx_extras.lrucache bx_extras.pstat bx_extras.stats

mtime() (bx_extras.lrucache.LRUCache method) MultiIndexed (class in bx.align.axt) (in module bx.align.maf)

N

n_block_sizes (bx.seq.twobit.TwoBitSequence attribute) n_block_starts (bx.seq.twobit.TwoBitSequence attribute) NeighborTestCase (class in bx.intervals.intersection_tests) new() (bx.interval_index_file.Index method) new_bits() (bx.bitset_tests.BinnedBitSetTests method) (bx.bitset_tests.BitSetTests method) NewickParser (class in bx.phylo.newick) next_clear() (bx.bitset.BinnedBitSet method) (bx.bitset.BitSet method) next_motif() (bx.motif.io.transfac.TransfacReader method) next_set() (bx.bitset.BinnedBitSet method) (bx.bitset.BitSet method)

NibFile (class in bx.seq.nib) NibReader (class in bx.seq.nib) NIBTestCase (class in bx.seq.nib_tests) NibWriter (class in bx.seq.nib) NiceReaderWrapper (class in bx.intervals.io) no_leaves (bx.arrays.array_tree.ArrayTree attribute) nonCpG (class in bx.align.sitemask.cpg) nonrepeats() (in module bx_extras.pstat) nonzero() (in module bx.cookbook.doc_optparse) NQS (class in bx.align.sitemask.quality)

O

open() (bx.bbi.bbi_file.BBIFile method) (bx.interval_index_file.Index method) (bx.interval_index_file.Indexes method) open_compressed() (in module bx.misc)

open_data() (bx.align.maf.MAFIndexedAccess method) open_seqs() (bx.align.lav.Reader method) outputpairedstats() (in module bx_extras.stats) overwrite_start_end() (in module bx.intervals.random_intervals)

P

pack() (bx.misc.binary_file.BinaryFileWriter method) pack_and_write() (bx.misc.binary_file.BinaryFileWriter method) parse() (in module bx.cookbook.doc_optparse) parse_a_stanza() (bx.align.lav.Reader method) parse_actions (bx.motif.io.transfac.TransfacReader attribute) parse_attributes() (in module bx.align.maf) parse_comment() (bx.tabular.io.TableReader method) parse_h_stanza() (bx.align.lav.Reader method) parse_header() (bx.tabular.io.TableReader method) (in module bx.arrays.wiggle) (in module bx.wiggle) parse_record() (bx.motif.io.transfac.TransfacReader method) parse_row() (bx.intervals.io.GenomicIntervalReader method) (bx.tabular.io.TableReader method) parse_s_seq() (bx.align.lav.Reader method) parse_s_stanza() (bx.align.lav.Reader method) parse_string() (bx.phylo.newick.NewickParser method)

parse_unknown_stanza() (bx.align.lav.Reader method) parse_weight() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) ParseError ParsingError path_to_src_name() (bx.align.lav.Reader method) Pipeline (class in bx.filter) pl() (in module bx_extras.pstat) popitem() (bx.cookbook.ImmutableDict method) PositionWeightMatrix (class in bx.pwm.position_weight_matrix) pretty() (bx.phylo.newick.Edge method) (bx.phylo.newick.Tree method) printcc() (in module bx_extras.pstat) printincols() (in module bx_extras.pstat) printl() (in module bx_extras.pstat) pseudocount() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) push_up() (bx.intervals.operations.find_clusters.ClusterNode method) pwm_score() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) PWMTestCase (class in bx.pwm.pwm_tests)

Q

QdnaCodebook (class in bx.seq.qdna) QdnaFile (class in bx.seq.qdna) QdnaReader (class in bx.seq.qdna)

QDNATestCase (class in bx.seq.qdna_tests) QdnaWriter (class in bx.seq.qdna) query() (bx.bbi.bbi_file.BBIFile method)

R

r_find() (bx.bbi.bpt_file.BPTFile method) r_find_overlapping() (bx.bbi.cirtree_file.CIRTreeFile method) r_find_overlapping_leaf() (bx.bbi.cirtree_file.CIRTreeFile method) r_find_overlapping_parent() (bx.bbi.cirtree_file.CIRTreeFile method) raw_fetch() (bx.seq.nib.NibFile method) (bx.seq.qdna.QdnaFile method) (bx.seq.seq.SeqFile method) rc_or_nothing() (in module bx.align.lav) read() (bx.misc.bgzf.BGZFFile method) (bx.misc.binary_file.BinaryFileReader method) (bx.misc.seekbzip2.SeekableBzip2File method) (bx.misc.seeklzop.SeekableLzopFile method) (bx.misc.seeklzop.UnpackWrapper method) (bx.seq.twobit.TwoBitFile method) read_and_unpack() (bx.misc.binary_file.BinaryFileReader method) read_as_basic() (bx.pwm.position_weight_matrix.Reader method) read_as_transfac() (bx.pwm.position_weight_matrix.Reader method) read_at_current_offset() (bx.align.maf.MAFIndexedAccess method) read_block_coords() (bx.seq.twobit.TwoBitFile method) read_c_string() (bx.misc.binary_file.BinaryFileReader method) read_codebook() (bx.seq.qdna.QdnaCodebook method) read_float() (bx.misc.binary_file.BinaryFileReader method) read_lengths_file() (in module bx.misc.readlengths) read_next_axt() (in module bx.align.axt) read_next_maf() (in module bx.align.maf) read_p_string() (bx.seq.twobit.TwoBitFile method) read_packed() (in module bx.binned_array) read_raw_array() (bx.misc.binary_file.BinaryFileReader method) read_scoring_scheme() (in module bx.align.score) read_string() (bx.seq.qdna.QdnaFile method) read_uint16() (bx.misc.binary_file.BinaryFileReader method) read_uint32() (bx.misc.binary_file.BinaryFileReader method) read_uint64() (bx.misc.binary_file.BinaryFileReader method) read_uint8() (bx.misc.binary_file.BinaryFileReader method) readable() (bx.misc.seekbzip2.SeekableBzip2File method) (bx.misc.seeklzop.SeekableLzopFile method) (in module bx.cookbook.attribute) Reader (class in bx.align.axt) (class in bx.align.lav) (class in bx.align.maf) (class in bx.pwm.position_weight_matrix) (class in bx.wiggle)

ReaderIter (class in bx.align.axt) (class in bx.align.lav) (class in bx.align.maf) readline() (bx.misc.filecache.FileCache method) (bx.misc.seekbzip2.SeekableBzip2File method) (bx.misc.seeklzop.SeekableLzopFile method) (in module bx.align.axt) (in module bx.align.maf) readlines() (bx.misc.seekbzip2.SeekableBzip2File method) recode() (in module bx_extras.pstat) reduction_level (bx.bbi.bbi_file.ZoomLevel attribute) remap() (in module bx_extras.pstat) remove() (bx.filter.Pipeline method) remove_all_gap_columns() (bx.align.core.Alignment method) replace() (in module bx_extras.pstat) Restricted (class in bx.align.sitemask.cpg) reverse_complement() (bx.align.core.Alignment method) (bx.align.core.Component method) (bx.motif.pwm.BaseMatrix method) (bx.seq.seq.SeqFile method) (in module bx.pwm.position_weight_matrix) (in module bx.seq) (in module bx.seq.core) right() (bx.intervals.intersection.IntervalNode method) (bx.intervals.IntervalNode method) right_node (bx.intervals.intersection.IntervalNode attribute) (bx.intervals.IntervalNode attribute) root (bx.arrays.array_tree.ArrayTree attribute) root_node (bx.intervals.intersection.IntervalNode attribute) (bx.intervals.IntervalNode attribute) rotateleft() (bx.intervals.operations.find_clusters.ClusterNode method) (bx.intervals.operations.quicksect.IntervalNode method) rotateright() (bx.intervals.operations.find_clusters.ClusterNode method) (bx.intervals.operations.quicksect.IntervalNode method) roundlist() (in module bx_extras.pstat) rsquared() (in module bx.pwm.position_weight_matrix) run() (bx.filter.Filter method)

S

s_stanza() (bx.align.lav.Reader method) scaled() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) score (bx.align.core.Alignment property) score_align() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) score_align_gaps() (in module bx.pwm.position_weight_matrix) score_align_motif() (in module bx.pwm.position_weight_matrix) score_alignment() (bx.align.score.ScoringScheme method) (in module bx.align.score) score_quantum_seq() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) score_reverse_seq() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) score_seq() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) score_string() (bx.motif.pwm.ScoringMatrix method) score_string_with_gaps() (bx.motif.pwm.ScoringMatrix method) score_texts() (bx.align.score.ScoringScheme method) (in module bx.align.score) ScoringMatrix (class in bx.motif.pwm) ScoringScheme (class in bx.align.score) second_mapping_from_file() (in module bx.seqmapping) seek() (bx.misc.bgzf.BGZFFile method) (bx.misc.binary_file.BinaryFileReader method) (bx.misc.binary_file.BinaryFileWriter method) (bx.misc.filecache.FileCache method) (bx.misc.seekbzip2.SeekableBzip2File method) (bx.misc.seeklzop.SeekableLzopFile method) seekable() (bx.misc.seekbzip2.SeekableBzip2File method) (bx.misc.seeklzop.SeekableLzopFile method) SeekableBzip2File (class in bx.misc.seekbzip2) SeekableLzopFile (class in bx.misc.seeklzop) seq_file() (in module bx.seq) (in module bx.seq.core) seq_reader() (in module bx.seq) (in module bx.seq.core) seq_writer() (in module bx.seq) (in module bx.seq.core) SeqFile (class in bx.seq.seq) SeqReader (class in bx.seq.seq) SeqReaderIter (class in bx.seq.seq) SEQTestCase (class in bx.seq.seq_tests) set() (bx.binned_array.BinnedArray method) (bx.bitset.BinnedBitSet method) (bx.bitset.BitSet method) set_fields() (bx.tabular.io.Header method) set_property() (bx.seq.qdna.QdnaFile method) set_range() (bx.arrays.array_tree.ArrayTree method) (bx.bitset.BinnedBitSet method) (bx.bitset.BitSet method) set_score() (bx.align.core.Alignment method) (bx.align.score.ScoringScheme method) set_src_size() (bx.align.core.Component method) set_text() (bx.seq.seq.SeqFile method) setdefault() (bx.cookbook.ImmutableDict method) setUp() (bx.align.epo_tests.TestBed method) (bx.align.epo_tests.TestEpo method) (bx.arrays.array_tree_tests.TestArrayTree method) (bx.intervals.cluster_tests.TestCluster method) (bx.intervals.intersection_tests.IntervalTreeTest method) (bx.intervals.intersection_tests.LotsaTestCase method) (bx.intervals.intersection_tests.NeighborTestCase method) (bx.intervals.intersection_tests.UpDownStreamTestCase method)

shuffle_columns() (in module bx.align.core) Simple (class in bx.align.sitemask.quality) simple_probability() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) simpleabut() (in module bx_extras.pstat) size (bx.bbi.bbi_file.SummarizedData attribute) (bx.bitset.BinnedBitSet attribute) (bx.bitset.BitSet attribute) (bx_extras.lrucache.LRUCache attribute) skip() (bx.binned_array.BinnedArrayWriter method) (bx.misc.binary_file.BinaryFileReader method) (bx.misc.binary_file.BinaryFileWriter method) slice() (bx.align.core.Alignment method) (bx.align.core.Component method) (bx.align.epo.Chain method) slice_by_component() (bx.align.core.Alignment method) slice_by_coord() (bx.align.core.Component method) slide_correlation() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) sort_keys_by_chrom() (in module bx.align.lav) sortby() (in module bx_extras.pstat) src_merge() (in module bx.align.core) src_size (bx.align.core.Component property) src_size() (bx.align.core.Alignment method) src_split() (in module bx.align.core) start (bx.bbi.bbi_file.SummarizedData attribute) (bx.bbi.bbi_file.SummaryBlock attribute) (bx.intervals.intersection.Interval attribute) (bx.intervals.intersection.IntervalNode attribute) (bx.intervals.Interval attribute) (bx.intervals.IntervalNode attribute) step() (bx.filter.Filter method) strand (bx.intervals.intersection.Interval attribute) (bx.intervals.Interval attribute) StrandFormatError subtract() (in module bx.intervals.operations.subtract) sum_data (bx.bbi.bbi_file.SummarizedData attribute) (bx.bbi.bbi_file.SummaryBlock attribute) sum_of_squares() (in module bx.pwm.position_weight_matrix) sum_squares (bx.bbi.bbi_file.SummarizedData attribute) (bx.bbi.bbi_file.SummaryBlock attribute) summarize() (bx.bbi.bbi_file.BBIFile method) summarize_from_full() (bx.bbi.bbi_file.BBIFile method) SummarizedData (class in bx.bbi.bbi_file) SummarizingBlockHandler (class in bx.bbi.bigbed_file) (class in bx.bbi.bigwig_file) SummaryBlock (class in bx.bbi.bbi_file) sym_to_char() (in module bx.align.score) symbols (bx.pwm.position_weight_matrix.PositionWeightMatrix attribute)

T

TableReader (class in bx.tabular.io) TableRow (class in bx.tabular.io) tell() (bx.misc.bgzf.BGZFFile method) (bx.misc.binary_file.BinaryFileReader method) (bx.misc.binary_file.BinaryFileWriter method) (bx.misc.seekbzip2.SeekableBzip2File method) (bx.misc.seeklzop.SeekableLzopFile method) test() (in module bx.misc.cdb_tests) (in module bx_extras.fpconst) test_access() (bx.bitset_tests.AbstractTests method) test_accumulate() (bx.align.score_tests.BasicTests method) test_align() (bx.align.score_tests.BasicTests method) test_and() (bx.bitset_tests.AbstractTests method) test_another() (bx.intervals.cluster_tests.TestCluster method) test_asymm_scoring() (bx.align.score_tests.BasicTests method) test_bgzf() (in module bx.misc.bgzf_tests) test_big() (bx.arrays.array_tree_tests.TestArrayTree method) test_ci() (bx.align.epo_tests.TestBed method) test_column_iter() (in module bx.align.maf_tests) test_count() (bx.bitset_tests.AbstractTests method) (bx.intervals.intersection_tests.LotsaTestCase method) test_cpg_inclusive() (in module bx.align.sitemask.sitemask_tests) test_cpg_restricted() (in module bx.align.sitemask.sitemask_tests) test_create() (in module bx.motif.pwm_tests) test_distance() (bx.intervals.cluster_tests.TestCluster method) test_DNA() (bx.seqmapping_tests.CharMappingTests method) test_DNA_list() (bx.seqmapping_tests.CharMappingTests method) test_downstream() (bx.intervals.intersection_tests.UpDownStreamTestCase method) test_duplicates() (bx.intervals.cluster_tests.TestCluster method) test_easymerge() (bx.intervals.cluster_tests.TestCluster method) test_elem_u() (bx.align.epo_tests.TestBed method) test_empty() (bx.intervals.intersection_tests.IntervalTreeTest method) test_find() (bx.bitset_tests.AbstractTests method) (bx.intervals.intersection_tests.IntervalTreeTest method) (bx.intervals.intersection_tests.LotsaTestCase method) test_func() (in module bx.intervals.operations.quicksect) test_get() (bx.seq.fasta_tests.FASTATestCase method) (bx.seq.nib_tests.NIBTestCase method) (bx.seq.qdna_tests.QDNATestCase method) test_get_fasta() (bx.seq.seq_tests.SEQTestCase method) test_get_frequencies() (bx.arrays.array_tree_tests.TestArrayTree method) test_get_leaf() (bx.arrays.array_tree_tests.TestArrayTree method) test_get_nib() (bx.seq.seq_tests.SEQTestCase method) test_get_qdna() (bx.seq.seq_tests.SEQTestCase method) test_get_reader() (bx.seq.seq_tests.SEQTestCase method) test_get_summary() (bx.arrays.array_tree_tests.TestArrayTree method) test_hardmerge() (bx.intervals.cluster_tests.TestCluster method) test_higher_level_than_tree() (bx.arrays.array_tree_tests.TestArrayTree method) test_interval_index_file() (in module bx.interval_index_file_tests) test_interval_reader() (bx.wiggle_tests.TestWiggleReader method) test_isFinite() (in module bx_extras.fpconst) test_isInf() (in module bx_extras.fpconst) test_isNaN() (in module bx_extras.fpconst) test_isNegInf() (in module bx_extras.fpconst) test_isPosInf() (in module bx_extras.fpconst) test_large_sorted() (bx.intervals.cluster_tests.TestCluster method) test_larger() (bx.intervals.cluster_tests.TestCluster method) test_largescale() (bx.seqmapping_tests.AlignmentMappingTests method) test_left() (bx.intervals.intersection_tests.NeighborTestCase method) test_make_chain() (bx.align.epo_tests.TestEpo method) test_max_dist() (bx.intervals.intersection_tests.LotsaTestCase method) test_merge_case() (bx.intervals.cluster_tests.TestCluster method) test_merge_left_right() (bx.intervals.cluster_tests.TestCluster method) test_minregions() (bx.intervals.cluster_tests.TestCluster method) test_n() (bx.intervals.intersection_tests.UpDownStreamTestCase method) test_non_cpg() (in module bx.align.sitemask.sitemask_tests) test_none() (bx.intervals.cluster_tests.TestCluster method) test_nonsymm_scoring() (bx.align.score_tests.BasicTests method)

test_not() (bx.bitset_tests.AbstractTests method) test_offsets() (in module bx.interval_index_file_tests) test_or() (bx.bitset_tests.AbstractTests method) test_other() (bx.seqmapping_tests.CharMappingTests method) test_out() (bx.align.epo_tests.TestEpo method) test_overflow_access() (bx.bitset_tests.AbstractTests method) test_overflow_create() (bx.bitset_tests.AbstractTests method) test_parser() (in module bx.phylo.phast_tests) test_public_interval() (bx.intervals.intersection_tests.IntervalTreeTest method) test_range_access() (bx.bitset_tests.AbstractTests method) test_read_with_synteny() (in module bx.align.maf_tests) test_reader() (bx.wiggle_tests.TestWiggleReader method) (in module bx.align.maf_tests) (in module bx.motif.io.transfac_tests) test_rem_dash() (bx.align.epo_tests.TestEpo method) test_remove_all_gap_column() (in module bx.align.maf_tests) test_reverse_complement() (in module bx.align.maf_tests) test_right() (bx.intervals.intersection_tests.NeighborTestCase method) test_scoring() (in module bx.motif.pwm_tests) test_scoring_text() (bx.align.score_tests.BasicTests method) test_scoring_with_gaps() (in module bx.motif.pwm_tests) test_simple() (bx.seqmapping_tests.IntMappingTests method) test_slice() (in module bx.align.maf_tests) test_startbeforeend() (bx.intervals.cluster_tests.TestCluster method) test_toomany() (bx.intervals.intersection_tests.NeighborTestCase method) test_traverse() (bx.intervals.intersection_tests.IntervalTreeTest method) test_trivial() (bx.intervals.cluster_tests.TestCluster method) test_upstream() (bx.intervals.intersection_tests.UpDownStreamTestCase method) test_write_with_synteny() (in module bx.align.maf_tests) test_writer() (in module bx.align.maf_tests) test_wrong_dictkey() (bx.arrays.array_tree_tests.TestArrayTree method) test_zero() (in module bx.interval_index_file_tests) TestArrayTree (class in bx.arrays.array_tree_tests) TestBed (class in bx.align.epo_tests) TestCluster (class in bx.intervals.cluster_tests) TestEpo (class in bx.align.epo_tests) testReader() (bx.align.lav_tests.lavTestCase method) (bx.pwm.pwm_tests.PWMTestCase method) TestWiggleReader (class in bx.wiggle_tests) thread() (in module bx.align.tools.thread) throw_random_bits() (in module bx.intervals.random_intervals) throw_random_gap_list() (in module bx.intervals.random_intervals) throw_random_intervals() (in module bx.intervals.random_intervals) throw_random_list() (in module bx.intervals.random_intervals) throw_random_private() (in module bx.intervals.random_intervals) tile_interval() (in module bx.align.tools) (in module bx.align.tools.tile) to_count_matrix() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) to_file() (bx.arrays.array_tree.ArrayTree method) (bx.binned_array.BinnedArray method) (bx.misc.cdb.FileCDBDict class method) to_logodds_scoring_matrix() (bx.motif.pwm.FrequencyMatrix method) to_matrix() (bx.pwm.position_weight_matrix.PositionWeightMatrix method) to_stormo_scoring_matrix() (bx.motif.pwm.FrequencyMatrix method) toCigar() (in module bx.align.epo_tests) TransfacMotif (class in bx.motif.io.transfac) TransfacReader (class in bx.motif.io.transfac) TransfacWriter (class in bx.motif.io.transfac) traverse() (bx.intervals.intersection.IntervalNode method) (bx.intervals.intersection.IntervalTree method) (bx.intervals.IntervalNode method) (bx.intervals.IntervalTree method) (bx.intervals.operations.quicksect.IntervalNode method) (bx.intervals.operations.quicksect.IntervalTree method) Tree (class in bx.phylo.newick) TreeModel (class in bx.phylo.phast) TwoBitFile (class in bx.seq.twobit) TwoBitSequence (class in bx.seq.twobit)

U

unique() (in module bx_extras.pstat) unpack() (bx.misc.binary_file.BinaryFileReader method) UnpackWrapper (class in bx.misc.seeklzop)

update() (bx.cookbook.ImmutableDict method) UpDownStreamTestCase (class in bx.intervals.intersection_tests) upstream_of_interval() (bx.intervals.intersection.IntervalTree method) (bx.intervals.IntervalTree method)

V

valid_count (bx.bbi.bbi_file.SummarizedData attribute) (bx.bbi.bbi_file.SummaryBlock attribute) value (bx.intervals.intersection.Interval attribute) (bx.intervals.Interval attribute)

value_size (bx.interval_index_file.Index property) vector_text() (bx.seq.qdna.QdnaCodebook method) version (bx.bbi.bbi_file.BBIFile attribute)

W

where() (bx.pwm.position_weight_matrix.Reader method) width (bx.motif.pwm.BaseMatrix property) WiggleReader (class in bx.arrays.wiggle) writable() (bx.misc.seekbzip2.SeekableBzip2File method) (bx.misc.seeklzop.SeekableLzopFile method) (in module bx.cookbook.attribute) write() (bx.align.axt.Writer method) (bx.align.lav.Writer method) (bx.align.maf.Writer method) (bx.align.tools.fuse.FusingAlignmentWriter method) (bx.align.tools.FusingAlignmentWriter method) (bx.binned_array.BinnedArrayWriter method) (bx.interval_index_file.Index method) (bx.interval_index_file.Indexes method) (bx.misc.binary_file.BinaryFileWriter method) (bx.motif.io.transfac.TransfacWriter method) (bx.seq.fasta.FastaWriter method) (bx.seq.nib.NibWriter method) (bx.seq.qdna.QdnaWriter method)

write_a_stanza() (bx.align.lav.Writer method) write_c_string() (bx.misc.binary_file.BinaryFileWriter method) write_h_stanza() (bx.align.lav.Writer method) write_header() (bx.binned_array.BinnedArrayWriter method) write_index() (bx.binned_array.BinnedArrayWriter method) write_lav_marker() (bx.align.lav.Writer method) write_packed() (in module bx.binned_array) write_raw_array() (bx.misc.binary_file.BinaryFileWriter method) write_s_stanza() (bx.align.lav.Writer method) write_trailer() (bx.align.lav.Writer method) write_uint16() (bx.misc.binary_file.BinaryFileWriter method) write_uint32() (bx.misc.binary_file.BinaryFileWriter method) write_uint64() (bx.misc.binary_file.BinaryFileWriter method) write_uint8() (bx.misc.binary_file.BinaryFileWriter method) writecc() (in module bx_extras.stats) Writer (class in bx.align.axt) (class in bx.align.lav) (class in bx.align.maf)

X

xreadlines() (bx.misc.seekbzip2.SeekableBzip2File method)

Z

zoom_levels (bx.bbi.bbi_file.BBIFile attribute)

ZoomLevel (class in bx.bbi.bbi_file)