rnalib
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rnalib
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Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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Y
_
__init__() (rnalib.AnnotationIterator method)
A
AbstractFeatureFilter (class in rnalib)
add() (rnalib.Transcriptome method)
add_contig_headers() (in module rnalib.utils)
alias() (rnalib.RefDict method)
aligns_to() (in module rnalib.utils)
all_equal() (in module rnalib.utils)
alt (rnalib.VcfRecord attribute)
annotate() (rnalib.Transcriptome method)
annotate_with_mygene() (rnalib.Transcriptome method)
AnnotationIterator (class in rnalib)
Archs4Dataset (class in rnalib.interfaces)
AutoDict (class in rnalib.utils)
B
BAM_FDUP (rnalib.constants.BamFlag attribute)
BAM_FMREVERSE (rnalib.constants.BamFlag attribute)
BAM_FMUNMAP (rnalib.constants.BamFlag attribute)
BAM_FPAIRED (rnalib.constants.BamFlag attribute)
BAM_FPROPER_PAIR (rnalib.constants.BamFlag attribute)
BAM_FQCFAIL (rnalib.constants.BamFlag attribute)
BAM_FREAD1 (rnalib.constants.BamFlag attribute)
BAM_FREAD2 (rnalib.constants.BamFlag attribute)
BAM_FREVERSE (rnalib.constants.BamFlag attribute)
BAM_FSECONDARY (rnalib.constants.BamFlag attribute)
BAM_FUNMAP (rnalib.constants.BamFlag attribute)
BAM_SUPPLEMENTARY (rnalib.constants.BamFlag attribute)
BamFlag (class in rnalib.constants)
BamWriter (class in rnalib.utils)
BedGraphIterator (class in rnalib)
BedIterator (class in rnalib)
BedRecord (class in rnalib)
bgzip_and_tabix() (in module rnalib.utils)
BigBedIterator (class in rnalib)
BigBedRecord (class in rnalib)
BigWigIterator (class in rnalib)
BioframeIterator (class in rnalib)
block_count (rnalib.BedRecord attribute)
block_sizes (rnalib.BedRecord attribute)
block_starts (rnalib.BedRecord attribute)
build() (rnalib.Transcriptome method)
build_amplicon_resources() (in module rnalib.tools)
C
calc_3end() (in module rnalib.utils)
calc_set_overlap() (in module rnalib.utils)
CANONICAL_CHROMOSOMES (in module rnalib.constants)
check_list() (in module rnalib.utils)
chromosome (rnalib.Feature attribute)
(rnalib.GI attribute)
(rnalib.GI_dataclass attribute)
chromosomes (rnalib.LocationIterator attribute)
chromosomes() (rnalib.RefDict method)
chromosomes_orig() (rnalib.RefDict method)
clear_annotations() (rnalib.Transcriptome method)
close() (rnalib.AnnotationIterator method)
(rnalib.GroupedLocationIterator method)
(rnalib.LocationIterator method)
(rnalib.PybedtoolsIterator method)
(rnalib.utils.BamWriter method)
cmp_sets() (in module rnalib.utils)
complement() (in module rnalib.utils)
convert_size() (in module rnalib.utils)
copy() (rnalib.GI method)
(rnalib.GI_dataclass method)
count_gc() (in module rnalib.utils)
count_lines() (in module rnalib.utils)
count_reads() (in module rnalib.utils)
count_rest() (in module rnalib.utils)
create_sub_class() (rnalib.Feature class method)
create_testdata() (in module rnalib.testdata)
cs_match() (rnalib.GI method)
(rnalib.GI_dataclass method)
D
data (rnalib.Item attribute)
DEFAULT_FLAG_FILTER (in module rnalib.constants)
describe() (rnalib.interfaces.Archs4Dataset method)
(rnalib.LocationIterator method)
(rnalib.TranscriptomeIterator method)
dir_tree() (in module rnalib.utils)
display_animated_gif() (in module rnalib.utils)
display_help() (in module rnalib.utils)
display_list() (in module rnalib.utils)
display_popover() (in module rnalib.utils)
display_textarea() (in module rnalib.utils)
distance() (rnalib.GI method)
(rnalib.GI_dataclass method)
download_bgzip_slice() (in module rnalib.testdata)
download_file() (in module rnalib.utils)
downsample_per_chrom() (in module rnalib.utils)
E
end (rnalib.Feature attribute)
(rnalib.GI attribute)
(rnalib.GI_dataclass attribute)
ensure_outdir() (in module rnalib.utils)
envelops() (rnalib.GI method)
(rnalib.GI_dataclass method)
execute_screencast() (in module rnalib.utils)
F
FastaIterator (class in rnalib)
FastPileupIterator (class in rnalib)
FastqIterator (class in rnalib)
FastqRead (class in rnalib.utils)
Feature (class in rnalib)
feature_id (rnalib.Feature attribute)
feature_type (rnalib.Feature attribute)
features() (rnalib.Feature method)
file (rnalib.LocationIterator attribute)
filter (rnalib.VcfRecord attribute)
filter() (rnalib.AbstractFeatureFilter method)
(rnalib.TranscriptFilter method)
(rnalib.utils.TagFilter method)
filter_if_no_tag (rnalib.utils.TagFilter attribute)
filter_tc() (in module rnalib.tools)
filter_values (rnalib.utils.TagFilter attribute)
find_all() (in module rnalib.utils)
find_attr_rec() (rnalib.Transcriptome method)
find_gpos() (in module rnalib.utils)
FixedKeyTypeDefaultdict (class in rnalib)
format (rnalib.VcfRecord attribute)
format_fasta() (in module rnalib.utils)
from_gi() (rnalib.Feature class method)
from_str() (rnalib.GI class method)
FTYPE_TO_SO (in module rnalib.constants)
fun_alias (rnalib.LocationIterator attribute)
G
gene_triples() (rnalib.Transcriptome method)
geneid2symbol() (in module rnalib.utils)
GeneSymbol (class in rnalib.utils)
get() (rnalib.Feature method)
get_aligned_blocks() (in module rnalib.utils)
get_archs4_sample_dict() (in module rnalib.utils)
get_bcgs() (in module rnalib.utils)
get_chromosomes() (rnalib.AbstractFeatureFilter method)
(rnalib.TranscriptFilter method)
get_config() (in module rnalib.utils)
get_counts() (rnalib.interfaces.Archs4Dataset method)
get_covered_contigs() (in module rnalib.utils)
get_downstream() (rnalib.GI method)
(rnalib.GI_dataclass method)
get_extended() (rnalib.GI method)
(rnalib.GI_dataclass method)
get_location() (rnalib.Feature method)
get_meta_keys() (rnalib.interfaces.Archs4Dataset method)
get_read_attr_info() (in module rnalib.utils)
get_resource() (in module rnalib.testdata)
get_rnk() (rnalib.Feature method)
get_sample_dict() (rnalib.interfaces.Archs4Dataset method)
get_sample_meta_keys() (in module rnalib.utils)
get_sample_metadata() (in module rnalib.utils)
(rnalib.interfaces.Archs4Dataset method)
get_sequence() (rnalib.Transcriptome method)
get_softclip_seq() (in module rnalib.utils)
get_softclipped_seq_and_qual() (in module rnalib.utils)
get_stranded() (rnalib.GI method)
(rnalib.GI_dataclass method)
get_struct() (rnalib.Transcriptome method)
get_tx_indices() (in module rnalib.utils)
get_unique_keys() (in module rnalib.utils)
get_upstream() (rnalib.GI method)
(rnalib.GI_dataclass method)
GFF3Iterator (class in rnalib)
GFF_FLAVOURS (in module rnalib.constants)
GI (class in rnalib)
gi() (in module rnalib)
GI_dataclass (class in rnalib)
group() (rnalib.LocationIterator method)
GroupedLocationIterator (class in rnalib)
grouper() (in module rnalib.utils)
gt2zyg() (in module rnalib.utils)
guess_file_format() (in module rnalib.utils)
gunzip() (in module rnalib.utils)
H
has_len() (rnalib.RefDict method)
head_counter() (in module rnalib.utils)
header() (rnalib.BigBedIterator method)
(rnalib.BigWigIterator method)
I
id (rnalib.VcfRecord attribute)
include_chromosomes() (rnalib.TranscriptFilter method)
include_gene_ids() (rnalib.TranscriptFilter method)
include_gene_types() (rnalib.TranscriptFilter method)
include_regions() (rnalib.TranscriptFilter method)
include_tags() (rnalib.TranscriptFilter method)
include_transcript_ids() (rnalib.TranscriptFilter method)
include_transcript_types() (rnalib.TranscriptFilter method)
index() (rnalib.RefDict method)
info (rnalib.VcfRecord attribute)
intersect_lists() (in module rnalib.utils)
inverse (rnalib.utils.TagFilter attribute)
is_adjacent() (rnalib.GI method)
(rnalib.GI_dataclass method)
is_empty() (rnalib.GI method)
(rnalib.GI_dataclass method)
is_stranded() (rnalib.GI method)
(rnalib.GI_dataclass method)
is_unbounded() (rnalib.GI method)
(rnalib.GI_dataclass method)
it() (in module rnalib)
Item (class in rnalib)
item_rgb (rnalib.BedRecord attribute)
iterate_data() (rnalib.FastaIterator method)
iterator() (rnalib.Transcriptome method)
K
key() (rnalib.Feature method)
kmer_search() (in module rnalib.utils)
L
left_match() (rnalib.GI method)
(rnalib.GI_dataclass method)
left_pos() (rnalib.GI method)
(rnalib.GI_dataclass method)
level (rnalib.BigBedRecord attribute)
list_resources() (in module rnalib.testdata)
load() (rnalib.RefDict static method)
(rnalib.Transcriptome class method)
load_annotations() (rnalib.Transcriptome method)
load_sequences() (rnalib.Transcriptome method)
location (rnalib.BedRecord attribute)
(rnalib.BigBedRecord attribute)
(rnalib.Item attribute)
(rnalib.LocationIterator attribute)
(rnalib.VcfRecord attribute)
LocationIterator (class in rnalib)
longest_GC_len() (in module rnalib.utils)
longest_hp_gc_len() (in module rnalib.utils)
M
make_random_intervals() (in module rnalib.testdata)
MAX_INT (in module rnalib.constants)
max_items() (rnalib.AnnotationIterator method)
(rnalib.BigBedIterator method)
(rnalib.BigWigIterator method)
(rnalib.FastaIterator method)
(rnalib.FastPileupIterator method)
(rnalib.GroupedLocationIterator method)
(rnalib.LocationIterator method)
(rnalib.MemoryIterator method)
(rnalib.MergedLocationIterator method)
(rnalib.PandasIterator method)
(rnalib.PybedtoolsIterator method)
(rnalib.ReadIterator method)
(rnalib.TabixIterator method)
(rnalib.TiledIterator method)
(rnalib.TranscriptomeIterator method)
MemoryIterator (class in rnalib)
merge() (rnalib.GI class method)
(rnalib.GI_dataclass class method)
(rnalib.LocationIterator method)
merge_and_validate() (rnalib.RefDict static method)
merge_bam_files() (in module rnalib.utils)
MergedLocationIterator (class in rnalib)
mm1 (rnalib.ReadPair attribute)
mm2 (rnalib.ReadPair attribute)
module
rnalib
rnalib.constants
rnalib.interfaces
rnalib.testdata
rnalib.tools
rnalib.utils
move_id_to_info_field() (in module rnalib.utils)
mygeneinfo_fields (in module rnalib.constants)
N
name (rnalib.BedRecord attribute)
(rnalib.BigBedRecord attribute)
(rnalib.utils.FastqRead attribute)
(rnalib.utils.GeneSymbol attribute)
norm_gn() (in module rnalib.utils)
O
open_file_obj() (in module rnalib.utils)
overlap() (rnalib.GI method)
(rnalib.GI_dataclass method)
overlaps() (rnalib.GI method)
(rnalib.GI_dataclass method)
P
pad_n() (in module rnalib.utils)
PairedReadIterator (class in rnalib)
PandasIterator (class in rnalib)
parent (rnalib.Feature attribute)
parse_gff_attributes() (in module rnalib.utils)
ParseMap (class in rnalib.utils)
per_position (rnalib.LocationIterator attribute)
plot_times() (in module rnalib.utils)
pos (rnalib.VcfRecord attribute)
print_dir_tree() (in module rnalib.utils)
print_fast5_tree() (in module rnalib.utils)
print_small_file() (in module rnalib.utils)
prune_tags() (in module rnalib.tools)
PybedtoolsIterator (class in rnalib)
PyrangesIterator (class in rnalib)
Q
qual (rnalib.utils.FastqRead attribute)
(rnalib.VcfRecord attribute)
query() (rnalib.Transcriptome method)
R
r1 (rnalib.ReadPair attribute)
r2 (rnalib.ReadPair attribute)
random_sample() (in module rnalib.utils)
read_alias_file() (in module rnalib.utils)
read_aligns_to_loc() (in module rnalib)
ReadIterator (class in rnalib)
ReadPair (class in rnalib)
ref (rnalib.VcfRecord attribute)
RefDict (class in rnalib)
refdict (rnalib.LocationIterator attribute)
region (rnalib.LocationIterator attribute)
remove_extension() (in module rnalib.utils)
reverse_complement() (in module rnalib.utils)
right_match() (rnalib.GI method)
(rnalib.GI_dataclass method)
right_pos() (rnalib.GI method)
(rnalib.GI_dataclass method)
rnalib
module
rnalib.constants
module
rnalib.interfaces
module
rnalib.testdata
module
rnalib.tools
module
rnalib.utils
module
rnd_seq() (in module rnalib.utils)
S
save() (rnalib.Transcriptome method)
save_annotations() (rnalib.Transcriptome method)
score (rnalib.BedRecord attribute)
(rnalib.BigBedRecord attribute)
score2 (rnalib.BigBedRecord attribute)
SEP (in module rnalib.constants)
seq (rnalib.utils.FastqRead attribute)
set_len() (rnalib.RefDict method)
set_region() (rnalib.LocationIterator method)
signif (rnalib.BigBedRecord attribute)
slice_from_parent() (rnalib.Transcriptome method)
slugify() (in module rnalib.utils)
sort() (rnalib.GI static method)
(rnalib.Transcriptome method)
sort_and_index_bam() (in module rnalib.utils)
split_by_maxwidth() (rnalib.GI method)
(rnalib.GI_dataclass method)
split_coordinates() (rnalib.GI method)
(rnalib.GI_dataclass method)
split_list() (in module rnalib.utils)
start (rnalib.Feature attribute)
(rnalib.GI attribute)
(rnalib.GI_dataclass attribute)
stats (rnalib.FastqIterator property)
(rnalib.LocationIterator property)
stats() (rnalib.AnnotationIterator method)
strand (rnalib.Feature attribute)
(rnalib.GI attribute)
(rnalib.GI_dataclass attribute)
subfeature_types (rnalib.Feature attribute)
symbol (rnalib.utils.GeneSymbol attribute)
T
TabixIterator (class in rnalib)
tag (rnalib.utils.TagFilter attribute)
tag_tc() (in module rnalib.tools)
TagFilter (class in rnalib.utils)
taxid (rnalib.utils.GeneSymbol attribute)
thick_end (rnalib.BedRecord attribute)
thick_start (rnalib.BedRecord attribute)
(rnalib.BigBedRecord attribute)
tile() (rnalib.LocationIterator method)
(rnalib.RefDict method)
TiledIterator (class in rnalib)
Timer (class in rnalib.utils)
to_bed() (rnalib.LocationIterator method)
(rnalib.MemoryIterator method)
(rnalib.Transcriptome method)
to_dataframe() (rnalib.LocationIterator method)
(rnalib.PandasIterator method)
(rnalib.TranscriptomeIterator method)
to_file_str() (rnalib.GI method)
(rnalib.GI_dataclass method)
to_gff3() (rnalib.Transcriptome method)
to_htseq() (rnalib.GI method)
(rnalib.GI_dataclass method)
to_intervaltrees() (rnalib.LocationIterator method)
to_list() (in module rnalib.utils)
(rnalib.FastqIterator method)
(rnalib.LocationIterator method)
to_pybedtools() (rnalib.GI method)
(rnalib.GI_dataclass method)
to_set() (in module rnalib.utils)
to_str() (in module rnalib.utils)
toggle_chr() (in module rnalib.utils)
TranscriptFilter (class in rnalib)
Transcriptome (class in rnalib)
transcriptome (rnalib.Feature attribute)
TranscriptomeIterator (class in rnalib)
U
update() (rnalib.AnnotationIterator method)
UrlretrieveTqdm (class in rnalib.utils)
V
VcfIterator (class in rnalib)
VcfRecord (class in rnalib)
W
write() (rnalib.utils.BamWriter method)
write_data() (in module rnalib.utils)
write_read() (rnalib.utils.BamWriter method)
Y
yield_unaligned_reads() (in module rnalib.utils)
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