Index

_

__getattr__() (bioat.lib.libcircos.Tcircle method) __getitem__() (bioat.lib.libcircos.Garc method) __init__() (bioat.lib.libcircos.Garc method) (bioat.lib.libcircos.Gcircle method) (bioat.lib.libcircos.Tarc method) (bioat.lib.libcircos.Tcircle method) (bioat.logger.LoggerManager method)

__setitem__() (bioat.lib.libcircos.Garc method) __str__() (bioat.exceptions.BioatError method)

A

about() (bioat.cli.Cli class method) add_garc() (bioat.lib.libcircos.Gcircle method)

add_stream_handler() (bioat.logger.LoggerManager method) add_tarc() (bioat.lib.libcircos.Tcircle method) Assembly (class in bioat.lib.libdataclasses)

B

bam (bioat.cli.Cli property) Bam (class in bioat.lib.libdataclasses) BamTools (class in bioat) (class in bioat.bamtools) barplot() (bioat.lib.libcircos.Gcircle method) bed (bioat.cli.Cli property) Bed (class in bioat.lib.libdataclasses) BedTools (class in bioat) (class in bioat.bedtools) bioat module bioat.about module bioat.bamtools module bioat.bedtools module bioat.cli module bioat.crisprtools module bioat.devtools module bioat.exceptions module bioat.fastxtools module bioat.foldtools module bioat.hictools module bioat.lib module bioat.lib.libalignment module bioat.lib.libcircos module bioat.lib.libcolor module bioat.lib.libcrispr module bioat.lib.libdataclasses module

bioat.lib.libdetect_seq module bioat.lib.libfastx module bioat.lib.libjgi module bioat.lib.libpandas module bioat.lib.libpatentseq module bioat.lib.libpath module bioat.lib.libpdb module bioat.lib.libphylo module bioat.lib.libplot module bioat.lib.libsnakemake module bioat.lib.libspider module bioat.logger module bioat.metatools module bioat.searchtools module bioat.systemtools module bioat.tabletools module bioat.target_seq module BioatError BioatFileFormatError BioatFileNotCompleteError BioatFileNotFoundError BioatInvalidInputError BioatInvalidOptionError BioatInvalidParameterError BioatMissingDependencyError BioatRuntimeError BioatValueError

C

calc_density() (bioat.lib.libcircos.Garc method) calc_nnratio() (bioat.lib.libcircos.Garc method) calc_nnskew() (bioat.lib.libcircos.Garc method) calculate_length_distribution() (in module bioat.lib.libfastx) cas13_finder() (bioat.CrisprTools method) (bioat.crisprtools.CrisprTools method) (in module bioat.crisprtools) (in module bioat.lib.libfastx) cas_finder() (bioat.CrisprTools method) (bioat.crisprtools.CrisprTools method) (in module bioat.crisprtools) (in module bioat.lib.libfastx) check_cmd() (in module bioat.lib.libpath) (in module bioat.lib.libsnakemake)

check_executable() (in module bioat.lib.libpath) check_read() (in module bioat.lib.libsnakemake) chord_plot() (bioat.lib.libcircos.Gcircle method) chromosome (bioat.lib.libdataclasses.Bed attribute) Cli (class in bioat.cli) cmaps (bioat.lib.libcircos.Gcircle attribute) cmp_align_list() (in module bioat.lib.libcrispr) colorlist (bioat.lib.libcircos.Garc attribute) colors (bioat.lib.libcircos.Gcircle attribute) contigs (bioat.lib.libdataclasses.Assembly attribute) convert_hex_to_rgb() (in module bioat.lib.libcolor) convert_rgb_to_hex() (in module bioat.lib.libcolor) crispr (bioat.cli.Cli property) CrisprTools (class in bioat) (class in bioat.crisprtools)

D

DEFAULT_CATEGORIES (bioat.lib.libjgi.JGIDoc attribute) DEFAULT_LEVEL (bioat.logger.LoggerManager attribute)

delete_proxy() (bioat.lib.libspider.ProxyPool method) download() (bioat.lib.libjgi.JGIOperator method)

E

end (bioat.lib.libdataclasses.Bed attribute)

extras (bioat.lib.libdataclasses.Fastq attribute)

F

Fasta (class in bioat.lib.libdataclasses) Fastq (class in bioat.lib.libdataclasses) fastx (bioat.cli.Cli property) FastxTools (class in bioat) (class in bioat.fastxtools) featureplot() (bioat.lib.libcircos.Gcircle method) FILENAME_CONFIG_PATH (bioat.lib.libjgi.JGIConfig attribute) FILENAME_COOKIE (bioat.lib.libjgi.JGIConfig attribute) FILENAME_TEMPLATE_LOG_FAIL (bioat.lib.libjgi.JGIConfig attribute)

FILENAME_TEMPLATE_XML (bioat.lib.libjgi.JGIConfig attribute) fillplot() (bioat.lib.libcircos.Gcircle method) filter_read_contains_n() (bioat.FastxTools method) (bioat.fastxtools.FastxTools method) fmt_this() (bioat.FastxTools method) (bioat.fastxtools.FastxTools method) fold (bioat.cli.Cli property) FoldTools (class in bioat) (class in bioat.foldtools) format_this_fastx() (in module bioat.lib.libfastx)

G

Garc (class in bioat.lib.libcircos) Gcircle (class in bioat.lib.libcircos) get_aligned_seq() (in module bioat.lib.libalignment) get_alignment_info() (in module bioat.lib.libalignment) get_best_alignment() (in module bioat.lib.libalignment) get_cut2ref_aln_info() (bioat.FoldTools method) (bioat.foldtools.FoldTools method) (in module bioat.lib.libpdb)

get_effective_resolutions() (bioat.HiCTools method) (bioat.hictools.HiCTools method) get_logger() (bioat.logger.LoggerManager static method) get_proxy() (bioat.lib.libspider.ProxyPool method) get_random_user_agents() (in module bioat.lib.libspider) google_scholar() (bioat.SearchTools method) (bioat.searchtools.SearchTools method)

H

header (bioat.lib.libdataclasses.Fasta attribute) (bioat.lib.libdataclasses.Fastq attribute) heatmap() (bioat.lib.libcircos.Gcircle method)

hic (bioat.cli.Cli property) HiCTools (class in bioat) (class in bioat.hictools)

I

init_matplotlib() (in module bioat.lib.libplot) input_user_info() (bioat.lib.libjgi.JGIConfig method)

instantiate_pairwise_aligner() (in module bioat.lib.libalignment) is_valid() (bioat.lib.libdataclasses.Fastq method)

J

JGI_query() (bioat.MetaTools method) (bioat.metatools.MetaTools method)

JGIConfig (class in bioat.lib.libjgi) JGIDoc (class in bioat.lib.libjgi) JGIOperator (class in bioat.lib.libjgi)

L

length (bioat.lib.libdataclasses.Assembly attribute) (bioat.lib.libdataclasses.Fasta property) lineplot() (bioat.lib.libcircos.Gcircle method) list() (bioat.cli.Cli method)

load_config() (bioat.lib.libjgi.JGIConfig method) load_structure() (in module bioat.lib.libpdb) LOG_FORMAT (bioat.logger.LoggerManager attribute) LoggerManager (class in bioat.logger)

M

make_color_list() (in module bioat.lib.libcolor) map_color() (in module bioat.lib.libcolor) map_colors_between_two() (in module bioat.lib.libcolor) merge() (bioat.TableTools method) (bioat.tabletools.TableTools method) meta (bioat.cli.Cli property) MetaTools (class in bioat) (class in bioat.metatools) mgi_parse_md5() (bioat.FastxTools method) (bioat.fastxtools.FastxTools method) module bioat bioat.about bioat.bamtools bioat.bedtools bioat.cli bioat.crisprtools bioat.devtools bioat.exceptions bioat.fastxtools bioat.foldtools bioat.hictools bioat.lib bioat.lib.libalignment bioat.lib.libcircos bioat.lib.libcolor bioat.lib.libcrispr bioat.lib.libdataclasses bioat.lib.libdetect_seq bioat.lib.libfastx bioat.lib.libjgi bioat.lib.libpandas bioat.lib.libpatentseq bioat.lib.libpath bioat.lib.libpdb bioat.lib.libphylo bioat.lib.libplot bioat.lib.libsnakemake bioat.lib.libspider bioat.logger bioat.metatools bioat.searchtools bioat.systemtools bioat.tabletools bioat.target_seq

mpileup2table() (bioat.BamTools method) (bioat.bamtools.BamTools method) mute() (bioat.logger.LoggerManager method)

N

name (bioat.lib.libdataclasses.Bed attribute)

P

parse_xml() (bioat.lib.libjgi.JGIOperator method) path (bioat.lib.libdataclasses.Assembly attribute) pdb2fasta() (bioat.FoldTools method) (bioat.foldtools.FoldTools method) plot_colortable() (in module bioat.lib.libcolor) (in module bioat.lib.libplot)

plot_highlight() (bioat.lib.libcircos.Tcircle method) plot_length_distribution() (bioat.FastxTools method) (bioat.fastxtools.FastxTools method) plot_tree() (bioat.lib.libcircos.Tcircle method) print_head() (in module bioat.lib.libsnakemake) profile() (in module bioat.devtools) ProxyPool (class in bioat.lib.libspider)

Q

quality (bioat.lib.libdataclasses.Fastq attribute) query() (bioat.lib.libjgi.JGIOperator method)

query_patent() (bioat.SearchTools method) (bioat.searchtools.SearchTools method)

R

region_heatmap() (bioat.target_seq.TargetSeq method) (bioat.TargetSeq method) region_heatmap_compare() (bioat.target_seq.TargetSeq method) (bioat.TargetSeq method)

remove_clip() (bioat.BamTools method) (bioat.bamtools.BamTools method) run() (in module bioat.lib.libpatentseq) run_target_seq_align() (in module bioat.lib.libcrispr)

S

save() (bioat.lib.libcircos.Gcircle method) save_config() (bioat.lib.libjgi.JGIConfig method) scatterplot() (bioat.lib.libcircos.Gcircle method) score (bioat.lib.libdataclasses.Bed attribute) search (bioat.cli.Cli property) SearchTools (class in bioat) (class in bioat.searchtools) select_blurb (bioat.lib.libjgi.JGIDoc attribute) sequence (bioat.lib.libdataclasses.Fasta attribute) (bioat.lib.libdataclasses.Fastq attribute) set_file() (bioat.logger.LoggerManager method) set_garcs() (bioat.lib.libcircos.Gcircle method) set_level() (bioat.logger.LoggerManager method) set_names() (bioat.logger.LoggerManager method)

set_option() (in module bioat.lib.libpandas) set_tarcs() (bioat.lib.libcircos.Tcircle method) setspine() (bioat.lib.libcircos.Gcircle method) setup_signal_handling() (in module bioat.bamtools) show_ref_cut() (bioat.FoldTools method) (bioat.foldtools.FoldTools method) (in module bioat.lib.libpdb) split() (bioat.TableTools method) (bioat.tabletools.TableTools method) start (bioat.lib.libdataclasses.Bed attribute) strand (bioat.lib.libdataclasses.Bed attribute) structure2string() (in module bioat.lib.libpdb) SystemTools (class in bioat) (class in bioat.systemtools)

T

table (bioat.cli.Cli property) table_hg38_chromosome_length() (in module bioat.lib.libcircos) table_hg38_cytoband() (in module bioat.lib.libcircos) table_mm10_chromosome_length() (in module bioat.lib.libcircos) table_mm10_cytoband() (in module bioat.lib.libcircos) TableTools (class in bioat) (class in bioat.tabletools)

Tarc (class in bioat.lib.libcircos) target_seq (bioat.cli.Cli property) TargetSeq (class in bioat) (class in bioat.target_seq) Tcircle (class in bioat.lib.libcircos) tickplot() (bioat.lib.libcircos.Gcircle method)

U

URL_JGI_FETCH_XML (bioat.lib.libjgi.JGIConfig attribute) URL_JGI_LOGIN (bioat.lib.libjgi.JGIConfig attribute)

URL_JGI_MAIN (bioat.lib.libjgi.JGIConfig attribute) usage_example_blurb (bioat.lib.libjgi.JGIDoc attribute)

V

VCF (class in bioat.lib.libdataclasses)

version() (bioat.cli.Cli class method)