bx-python
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Application Documentation
bx-python
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A
AbstractTests (class in bx.bitset_tests)
abut() (in module bx_extras.pstat)
accumulate_scores() (in module bx.align.score)
Action (class in bx.cookbook.argparse)
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)
add_argument() (bx.cookbook.argparse.HelpFormatter method)
add_arguments() (bx.cookbook.argparse.HelpFormatter method)
add_component() (bx.align.core.Alignment method)
add_interval() (bx.intervals.intersection.IntervalTree method)
add_subparsers() (bx.cookbook.argparse.ArgumentParser method)
add_text() (bx.cookbook.argparse.HelpFormatter method)
add_usage() (bx.cookbook.argparse.HelpFormatter method)
addParseAction() (bx_extras.pyparsing.ParserElement method)
after() (bx.intervals.intersection.IntervalTree method)
after_interval() (bx.intervals.intersection.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)
And (class in bx_extras.pyparsing)
append() (bx.filter.Pipeline method)
(bx_extras.pyparsing.ParseExpression method)
ArgumentDefaultsHelpFormatter (class in bx.cookbook.argparse)
ArgumentError
ArgumentParser (class in bx.cookbook.argparse)
ArgumentTypeError
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)
asDict() (bx_extras.pyparsing.ParseResults method)
asList() (bx_extras.pyparsing.ParseResults method)
assert_bits() (bx.bitset_tests.AbstractTests method)
asXML() (bx_extras.pyparsing.ParseResults 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)
before_interval() (bx.intervals.intersection.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.argparse
module
bx.cookbook.attribute
module
bx.cookbook.doc_optparse
module
bx.cookbook.progress_bar
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.pyparsing
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
CaselessKeyword (class in bx_extras.pyparsing)
CaselessLiteral (class in bx_extras.pyparsing)
cdbhash() (in module bx.misc.cdb)
CDSReader() (in module bx.gene_reader)
Chain (class in bx.align.epo)
CharMappingTests (class in bx.seqmapping_tests)
CharsNotIn (class in bx_extras.pyparsing)
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)
checkRecursion() (bx_extras.pyparsing.And method)
(bx_extras.pyparsing.Each method)
(bx_extras.pyparsing.MatchFirst method)
(bx_extras.pyparsing.Or method)
(bx_extras.pyparsing.ParseElementEnhance method)
(bx_extras.pyparsing.ParserElement method)
chop_list() (in module bx.align.tools.chop)
chrom (bx.intervals.intersection.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.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)
col() (in module bx_extras.pyparsing)
colex() (in module bx_extras.pstat)
collapse() (in module bx_extras.pstat)
column_iter() (bx.align.core.Alignment method)
Combine (class in bx_extras.pyparsing)
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)
convert_arg_line_to_args() (bx.cookbook.argparse.ArgumentParser method)
coord_to_col() (bx.align.core.Component method)
copy() (bx.intervals.io.GenomicInterval method)
(bx_extras.pyparsing.Forward method)
(bx_extras.pyparsing.Keyword method)
(bx_extras.pyparsing.ParserElement method)
(bx_extras.pyparsing.ParseResults 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)
countedArray() (in module bx_extras.pyparsing)
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_KEYWORD_CHARS (bx_extras.pyparsing.Keyword attribute)
DEFAULT_SIZE (in module bx_extras.lrucache)
DEFAULT_WHITE_CHARS (bx_extras.pyparsing.ParserElement attribute)
delimitedList() (in module bx_extras.pyparsing)
Dict (class in bx_extras.pyparsing)
dict_to_file() (bx.arrays.array_tree.FileArrayTreeDict class method)
dictOf() (in module bx_extras.pyparsing)
Dispatch (class in bx_extras.stats)
dm() (in module bx_extras.pstat)
do_path_subs() (in module bx.align.lav)
downcaseTokens() (in module bx_extras.pyparsing)
downstream_of_interval() (bx.intervals.intersection.IntervalTree method)
dtype (bx.arrays.array_tree.ArrayTree attribute)
dump() (bx_extras.pyparsing.ParseResults method)
duplicates() (in module bx_extras.pstat)
E
Each (class in bx_extras.pyparsing)
Edge (class in bx.phylo.newick)
Empty (class in bx_extras.pyparsing)
enablePackrat() (bx_extras.pyparsing.ParserElement static method)
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)
end_section() (bx.cookbook.argparse.HelpFormatter method)
EPOitem (class in bx.align.epo)
eps_logo() (in module bx.motif.logo)
error() (bx.cookbook.argparse.ArgumentParser method)
exception() (in module bx.cookbook.doc_optparse)
exit() (bx.cookbook.argparse.ArgumentParser method)
(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)
FileType (class in bx.cookbook.argparse)
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)
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)
FollowedBy (class in bx_extras.pyparsing)
format_help() (bx.cookbook.argparse.ArgumentParser method)
(bx.cookbook.argparse.HelpFormatter method)
format_tabular() (in module bx.align.maf)
(in module bx.pwm.maf_select_motifs)
format_usage() (bx.cookbook.argparse.ArgumentParser method)
format_version() (bx.cookbook.argparse.ArgumentParser method)
Forward (class in bx_extras.pyparsing)
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.fuse)
fuse_list() (in module bx.align.tools.fuse)
FusingAlignmentWriter (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)
(bx_extras.pyparsing.ParseResults 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.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)
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)
getException() (bx_extras.pyparsing.ParserElement method)
getintervals() (bx.intervals.operations.find_clusters.ClusterNode method)
getlines() (bx.intervals.cluster.ClusterTree method)
(bx.intervals.operations.find_clusters.ClusterNode method)
getName() (bx_extras.pyparsing.ParseResults method)
getregions() (bx.intervals.cluster.ClusterTree method)
getTokensEndLoc() (in module bx_extras.pyparsing)
GoToColumn (class in bx_extras.pyparsing)
Group (class in bx_extras.pyparsing)
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)
HelpFormatter (class in bx.cookbook.argparse)
I
iand() (bx.bitset.BinnedBitSet method)
(bx.bitset.BitSet method)
identity_mapping() (in module bx.seqmapping)
ignore() (bx_extras.pyparsing.Combine method)
(bx_extras.pyparsing.ParseElementEnhance method)
(bx_extras.pyparsing.ParseExpression method)
(bx_extras.pyparsing.ParserElement method)
ImmutableDict (class in bx.cookbook)
Inclusive (class in bx.align.sitemask.cpg)
indentedBlock() (in module bx_extras.pyparsing)
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.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.operations.find_clusters.ClusterNode method)
(bx.intervals.operations.quicksect.IntervalNode method)
(bx.intervals.operations.quicksect.IntervalTree method)
insert_interval() (bx.intervals.intersection.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.operations.quicksect.IntervalNode method)
(bx.intervals.operations.quicksect.IntervalTree method)
(in module bx.intervals.operations.intersect)
Intersecter (in module bx.intervals.intersection)
interval (bx.intervals.intersection.IntervalNode attribute)
Interval (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.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.tile)
IntervalTree (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)
items() (bx_extras.pyparsing.ParseResults method)
iterate() (bx.interval_index_file.Index method)
iterprogress() (in module bx.cookbook.progress_bar)
iterwrapper() (bx.intervals.io.NiceReaderWrapper method)
ixor() (bx.bitset.BitSet method)
J
join() (in module bx.intervals.operations.join)
K
keepOriginalText() (in module bx_extras.pyparsing)
keys() (bx_extras.pyparsing.ParseResults method)
Keyword (class in bx_extras.pyparsing)
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)
leaveWhitespace() (bx_extras.pyparsing.Forward method)
(bx_extras.pyparsing.ParseElementEnhance method)
(bx_extras.pyparsing.ParseExpression method)
(bx_extras.pyparsing.ParserElement method)
left() (bx.intervals.intersection.IntervalNode method)
left_node (bx.intervals.intersection.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)
line() (in module bx_extras.pyparsing)
linedelimited() (in module bx_extras.pstat)
LineEnd (class in bx_extras.pyparsing)
lineincols() (in module bx_extras.pstat)
lineincustcols() (in module bx_extras.pstat)
lineno() (in module bx_extras.pyparsing)
LineStart (class in bx_extras.pyparsing)
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)
Literal (class in bx_extras.pyparsing)
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)
loc (bx_extras.pyparsing.ParseBaseException attribute)
(bx_extras.pyparsing.ParseException attribute)
(bx_extras.pyparsing.ParseFatalException attribute)
(bx_extras.pyparsing.ParseSyntaxException attribute)
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)
makeHTMLTags() (in module bx_extras.pyparsing)
makelol() (in module bx_extras.pstat)
makestr() (in module bx_extras.pstat)
makeXMLTags() (in module bx_extras.pyparsing)
markInputline() (bx_extras.pyparsing.ParseBaseException method)
mask_columns() (in module bx.align.sitemask.cpg)
masked (bx.align.sitemask.core.MaskPipeline property)
masked_block_sizes (bx.seq.twobit.TwoBitSequence attribute)
masked_block_starts (bx.seq.twobit.TwoBitSequence attribute)
Masker (class in bx.align.sitemask.core)
MaskPipeline (class in bx.align.sitemask.core)
match_consensus() (in module bx.pwm.position_weight_matrix)
MatchFirst (class in bx_extras.pyparsing)
matchOnlyAtCol() (in module bx_extras.pyparsing)
matchPreviousExpr() (in module bx_extras.pyparsing)
matchPreviousLiteral() (in module bx_extras.pyparsing)
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.argparse
bx.cookbook.attribute
bx.cookbook.doc_optparse
bx.cookbook.progress_bar
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.pyparsing
bx_extras.stats
psyco_full
msg (bx_extras.pyparsing.ParseBaseException attribute)
(bx_extras.pyparsing.ParseException attribute)
(bx_extras.pyparsing.ParseFatalException attribute)
(bx_extras.pyparsing.ParseSyntaxException attribute)
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)
Namespace (class in bx.cookbook.argparse)
NeighborTestCase (class in bx.intervals.intersection_tests)
nestedExpr() (in module bx_extras.pyparsing)
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)
NoMatch (class in bx_extras.pyparsing)
nonCpG (class in bx.align.sitemask.cpg)
nonrepeats() (in module bx_extras.pstat)
nonzero() (in module bx.cookbook.doc_optparse)
NotAny (class in bx_extras.pyparsing)
NQS (class in bx.align.sitemask.quality)
nullDebugAction() (in module bx_extras.pyparsing)
O
oneOf() (in module bx_extras.pyparsing)
OneOrMore (class in bx_extras.pyparsing)
OnlyOnce (class in bx_extras.pyparsing)
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)
operatorPrecedence() (in module bx_extras.pyparsing)
Optional (class in bx_extras.pyparsing)
Or (class in bx_extras.pyparsing)
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_args() (bx.cookbook.argparse.ArgumentParser method)
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_known_args() (bx.cookbook.argparse.ArgumentParser method)
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)
ParseBaseException
ParseElementEnhance (class in bx_extras.pyparsing)
ParseError
ParseException
ParseExpression (class in bx_extras.pyparsing)
ParseFatalException
parseFile() (bx_extras.pyparsing.ParserElement method)
parseImpl() (bx_extras.pyparsing.And method)
(bx_extras.pyparsing.CaselessKeyword method)
(bx_extras.pyparsing.CaselessLiteral method)
(bx_extras.pyparsing.CharsNotIn method)
(bx_extras.pyparsing.Each method)
(bx_extras.pyparsing.FollowedBy method)
(bx_extras.pyparsing.GoToColumn method)
(bx_extras.pyparsing.Keyword method)
(bx_extras.pyparsing.LineEnd method)
(bx_extras.pyparsing.LineStart method)
(bx_extras.pyparsing.Literal method)
(bx_extras.pyparsing.MatchFirst method)
(bx_extras.pyparsing.NoMatch method)
(bx_extras.pyparsing.NotAny method)
(bx_extras.pyparsing.OneOrMore method)
(bx_extras.pyparsing.Optional method)
(bx_extras.pyparsing.Or method)
(bx_extras.pyparsing.ParseElementEnhance method)
(bx_extras.pyparsing.ParserElement method)
(bx_extras.pyparsing.QuotedString method)
(bx_extras.pyparsing.Regex method)
(bx_extras.pyparsing.SkipTo method)
(bx_extras.pyparsing.StringEnd method)
(bx_extras.pyparsing.StringStart method)
(bx_extras.pyparsing.White method)
(bx_extras.pyparsing.Word method)
(bx_extras.pyparsing.WordEnd method)
(bx_extras.pyparsing.WordStart method)
(bx_extras.pyparsing.ZeroOrMore method)
parserElement (bx_extras.pyparsing.ParseBaseException attribute)
(bx_extras.pyparsing.ParseException attribute)
(bx_extras.pyparsing.ParseFatalException attribute)
(bx_extras.pyparsing.ParseSyntaxException attribute)
ParserElement (class in bx_extras.pyparsing)
ParseResults (class in bx_extras.pyparsing)
parseString() (bx_extras.pyparsing.ParserElement method)
ParseSyntaxException
parseWithTabs() (bx_extras.pyparsing.ParserElement method)
ParsingError
path_to_src_name() (bx.align.lav.Reader method)
Pipeline (class in bx.filter)
pl() (in module bx_extras.pstat)
pop() (bx_extras.pyparsing.ParseResults method)
popitem() (bx.cookbook.ImmutableDict method)
PositionWeightMatrix (class in bx.pwm.position_weight_matrix)
postParse() (bx_extras.pyparsing.Combine method)
(bx_extras.pyparsing.Dict method)
(bx_extras.pyparsing.Group method)
(bx_extras.pyparsing.ParserElement method)
(bx_extras.pyparsing.Suppress method)
(bx_extras.pyparsing.Upcase method)
preParse() (bx_extras.pyparsing.GoToColumn method)
(bx_extras.pyparsing.LineStart method)
(bx_extras.pyparsing.ParserElement method)
pretty() (bx.phylo.newick.Edge method)
(bx.phylo.newick.Tree method)
print_help() (bx.cookbook.argparse.ArgumentParser method)
print_usage() (bx.cookbook.argparse.ArgumentParser method)
print_version() (bx.cookbook.argparse.ArgumentParser method)
printcc() (in module bx_extras.pstat)
printincols() (in module bx_extras.pstat)
printl() (in module bx_extras.pstat)
ProgressBar (class in bx.cookbook.progress_bar)
pseudocount() (bx.pwm.position_weight_matrix.PositionWeightMatrix method)
pstr (bx_extras.pyparsing.ParseBaseException attribute)
(bx_extras.pyparsing.ParseException attribute)
(bx_extras.pyparsing.ParseFatalException attribute)
(bx_extras.pyparsing.ParseSyntaxException attribute)
psyco_full
module
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)
QuotedString (class in bx_extras.pyparsing)
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)
RawDescriptionHelpFormatter (class in bx.cookbook.argparse)
RawTextHelpFormatter (class in bx.cookbook.argparse)
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)
RecursiveGrammarException
reduction_level (bx.bbi.bbi_file.ZoomLevel attribute)
Regex (class in bx_extras.pyparsing)
remap() (in module bx_extras.pstat)
remove() (bx.filter.Pipeline method)
remove_all_gap_columns() (bx.align.core.Alignment method)
removeQuotes() (in module bx_extras.pyparsing)
replace() (in module bx_extras.pstat)
replaceHTMLEntity() (in module bx_extras.pyparsing)
replaceWith() (in module bx_extras.pyparsing)
reset() (bx_extras.pyparsing.OnlyOnce method)
resetCache() (bx_extras.pyparsing.ParserElement static method)
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.core)
right() (bx.intervals.intersection.IntervalNode method)
right_node (bx.intervals.intersection.IntervalNode attribute)
root (bx.arrays.array_tree.ArrayTree attribute)
root_node (bx.intervals.intersection.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)
scanString() (bx_extras.pyparsing.ParserElement 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)
searchString() (bx_extras.pyparsing.ParserElement method)
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.core)
seq_reader() (in module bx.seq.core)
seq_writer() (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)
setBreak() (bx_extras.pyparsing.ParserElement method)
setDebug() (bx_extras.pyparsing.ParserElement method)
setDebugActions() (bx_extras.pyparsing.ParserElement method)
setdefault() (bx.cookbook.ImmutableDict method)
setDefaultKeywordChars() (bx_extras.pyparsing.Keyword static method)
setDefaultWhitespaceChars() (bx_extras.pyparsing.ParserElement static method)
setFailAction() (bx_extras.pyparsing.ParserElement method)
setName() (bx_extras.pyparsing.ParserElement method)
(bx_extras.pyparsing.Token method)
setParseAction() (bx_extras.pyparsing.ParserElement method)
setResultsName() (bx_extras.pyparsing.OneOrMore method)
(bx_extras.pyparsing.ParseExpression method)
(bx_extras.pyparsing.ParserElement method)
(bx_extras.pyparsing.ZeroOrMore 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)
setWhitespaceChars() (bx_extras.pyparsing.ParserElement 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)
SkipTo (class in bx_extras.pyparsing)
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)
srange() (in module bx_extras.pyparsing)
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)
start_section() (bx.cookbook.argparse.HelpFormatter method)
step() (bx.filter.Filter method)
strand (bx.intervals.intersection.Interval attribute)
StrandFormatError
streamline() (bx_extras.pyparsing.Forward method)
(bx_extras.pyparsing.ParseElementEnhance method)
(bx_extras.pyparsing.ParseExpression method)
(bx_extras.pyparsing.ParserElement method)
StringEnd (class in bx_extras.pyparsing)
StringStart (class in bx_extras.pyparsing)
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)
Suppress (class in bx_extras.pyparsing)
suppress() (bx_extras.pyparsing.ParserElement method)
(bx_extras.pyparsing.Suppress method)
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.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)
Token (class in bx_extras.pyparsing)
TokenConverter (class in bx_extras.pyparsing)
traceParseAction() (in module bx_extras.pyparsing)
TransfacMotif (class in bx.motif.io.transfac)
TransfacReader (class in bx.motif.io.transfac)
TransfacWriter (class in bx.motif.io.transfac)
transformString() (bx_extras.pyparsing.ParserElement method)
traverse() (bx.intervals.intersection.IntervalNode method)
(bx.intervals.intersection.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)
tryParse() (bx_extras.pyparsing.ParserElement method)
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)
Upcase (class in bx_extras.pyparsing)
upcaseTokens() (in module bx_extras.pyparsing)
update() (bx.cookbook.ImmutableDict method)
(bx.cookbook.progress_bar.ProgressBar method)
update_and_print() (bx.cookbook.progress_bar.ProgressBar method)
UpDownStreamTestCase (class in bx.intervals.intersection_tests)
upstream_of_interval() (bx.intervals.intersection.IntervalTree method)
V
valid_count (bx.bbi.bbi_file.SummarizedData attribute)
(bx.bbi.bbi_file.SummaryBlock attribute)
validate() (bx_extras.pyparsing.Forward method)
(bx_extras.pyparsing.ParseElementEnhance method)
(bx_extras.pyparsing.ParseExpression method)
(bx_extras.pyparsing.ParserElement method)
value (bx.intervals.intersection.Interval attribute)
value_size (bx.interval_index_file.Index property)
values() (bx_extras.pyparsing.ParseResults method)
vector_text() (bx.seq.qdna.QdnaCodebook method)
version (bx.bbi.bbi_file.BBIFile attribute)
W
where() (bx.pwm.position_weight_matrix.Reader method)
White (class in bx_extras.pyparsing)
whiteStrs (bx_extras.pyparsing.White attribute)
width (bx.motif.pwm.BaseMatrix property)
WiggleReader (class in bx.arrays.wiggle)
withAttribute() (in module bx_extras.pyparsing)
Word (class in bx_extras.pyparsing)
WordEnd (class in bx_extras.pyparsing)
WordStart (class in bx_extras.pyparsing)
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.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
ZeroOrMore (class in bx_extras.pyparsing)
zoom_levels (bx.bbi.bbi_file.BBIFile attribute)
ZoomLevel (class in bx.bbi.bbi_file)
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