Index
A
|
B
|
C
|
D
|
E
|
G
|
H
|
I
|
L
|
M
|
N
|
P
|
R
|
S
|
T
|
V
|
W
A
add_profile_actions() (in module dammit.profile)
B
BaseParser (class in dammit.fileio.base)
build_default_pipeline() (in module dammit.annotate)
(in module dammit.databases)
build_full_pipeline() (in module dammit.annotate)
build_nr_pipeline() (in module dammit.annotate)
build_quick_pipeline() (in module dammit.annotate)
(in module dammit.databases)
busco_to_df() (in module dammit.tasks.busco)
BuscoTask (class in dammit.tasks.busco)
C
check_hash() (in module dammit.tasks.shell)
check_or_fail() (in module dammit.databases)
check_parallel() (in module dammit.parallel)
check_uptodate() (dammit.handler.TaskHandler method)
checkbox() (in module dammit.ui)
ChunkParser (class in dammit.fileio.base)
clean_folder() (in module dammit.tasks.utils)
cleaned_actions() (in module dammit.utils)
clear_tasks() (dammit.handler.TaskHandler method)
CMPressTask (class in dammit.tasks.infernal)
cmscan_to_gff3() (in module dammit.fileio.gff3)
CMScanTask (class in dammit.tasks.infernal)
columns (dammit.fileio.gff3.GFF3Parser attribute)
(dammit.fileio.hmmer.HMMerParser attribute)
(dammit.fileio.infernal.InfernalParser attribute)
(dammit.fileio.maf.MafParser attribute)
convert() (dammit.fileio.gff3.GFF3Writer method)
convert_dtypes() (in module dammit.fileio.base)
D
dammit (module)
dammit.annotate (module)
dammit.app (module)
dammit.databases (module)
dammit.fileio (module)
dammit.fileio.base (module)
dammit.fileio.gff3 (module)
dammit.fileio.hmmer (module)
dammit.fileio.infernal (module)
dammit.fileio.maf (module)
dammit.handler (module)
dammit.log (module)
dammit.meta (module)
dammit.parallel (module)
dammit.profile (module)
dammit.tasks (module)
dammit.tasks.busco (module)
dammit.tasks.fastx (module)
dammit.tasks.gff (module)
dammit.tasks.hmmer (module)
dammit.tasks.infernal (module)
dammit.tasks.report (module)
dammit.tasks.shell (module)
dammit.tasks.transdecoder (module)
dammit.tasks.utils (module)
dammit.ui (module)
dammit.utils (module)
DammitApp (class in dammit.app)
DammitTask (class in dammit.utils)
decompose_attr_column() (dammit.fileio.gff3.GFF3Parser static method)
default_database_dir() (in module dammit.databases)
DependentTask (class in dammit.tasks.utils)
deps() (dammit.tasks.busco.BuscoTask method)
(dammit.tasks.hmmer.HMMPressTask method)
(dammit.tasks.hmmer.HMMScanTask method)
(dammit.tasks.infernal.CMPressTask method)
(dammit.tasks.infernal.CMScanTask method)
(dammit.tasks.transdecoder.TransDecoderLongOrfsTask method)
(dammit.tasks.transdecoder.TransDecoderPredictTask method)
(dammit.tasks.utils.DependentTask method)
description() (dammit.app.DammitApp method)
dict_to_task() (in module dammit.utils)
doit_task() (in module dammit.utils)
E
empty() (dammit.fileio.base.ChunkParser method)
(dammit.fileio.gff3.GFF3Parser method)
EmptyFile
epilog() (dammit.app.DammitApp method)
execute_task() (dammit.ui.GithubMarkdownReporter method)
G
generate_sequence_name() (in module dammit.tasks.report)
generate_sequence_summary() (in module dammit.tasks.report)
get_annotate_fasta_task() (in module dammit.tasks.report)
get_cat_task() (in module dammit.tasks.shell)
get_cmscan_gff3_task() (in module dammit.tasks.gff)
get_config() (in module dammit.meta)
get_download_and_gunzip_task() (in module dammit.tasks.shell)
get_download_and_untar_task() (in module dammit.tasks.shell)
get_download_task() (in module dammit.tasks.shell)
get_gff3_merge_task() (in module dammit.tasks.gff)
get_group_task() (in module dammit.tasks.utils)
get_gunzip_task() (in module dammit.tasks.shell)
get_handler() (in module dammit.annotate)
(in module dammit.databases)
get_hmmscan_gff3_task() (in module dammit.tasks.gff)
get_link_file_task() (in module dammit.tasks.shell)
get_maf_best_hits_task() (in module dammit.tasks.gff)
get_maf_gff3_task() (in module dammit.tasks.gff)
get_parser() (dammit.app.DammitApp method)
get_remap_hmmer_task() (in module dammit.tasks.hmmer)
get_rename_transcriptome_task() (in module dammit.tasks.fastx)
get_shmlast_gff3_task() (in module dammit.tasks.gff)
get_status() (dammit.handler.TaskHandler method)
get_transcriptome_stats_task() (in module dammit.tasks.fastx)
get_untargz_task() (in module dammit.tasks.shell)
GFF3Parser (class in dammit.fileio.gff3)
GFF3Writer (class in dammit.fileio.gff3)
GithubMarkdownReporter (class in dammit.ui)
H
handle_annotate() (dammit.app.DammitApp method)
handle_databases() (dammit.app.DammitApp method)
handle_migrate() (dammit.app.DammitApp method)
hashfile() (in module dammit.tasks.shell)
header() (in module dammit.ui)
HMMerParser (class in dammit.fileio.hmmer)
HMMPressTask (class in dammit.tasks.hmmer)
hmmscan_to_gff3() (in module dammit.fileio.gff3)
HMMScanTask (class in dammit.tasks.hmmer)
I
id_gen_wrapper() (in module dammit.fileio.gff3)
InfernalParser (class in dammit.fileio.infernal)
init_default_logger() (in module dammit.log)
install() (in module dammit.databases)
InstallationError
L
listing() (in module dammit.ui)
load_tasks() (dammit.handler.TaskHandler method)
M
maf_to_gff3() (in module dammit.fileio.gff3)
MafParser (class in dammit.fileio.maf)
mangle_coordinates() (dammit.fileio.gff3.GFF3Writer static method)
Move (class in dammit.utils)
N
next_ID() (in module dammit.fileio.gff3)
next_or_raise() (in module dammit.fileio.base)
P
paragraph() (in module dammit.ui)
parallel_fasta() (in module dammit.parallel)
parse_busco_full() (in module dammit.tasks.busco)
parse_busco_multiple() (in module dammit.tasks.busco)
parse_busco_summary() (in module dammit.tasks.busco)
print_meta() (in module dammit.databases)
print_statuses() (dammit.handler.TaskHandler method)
profile_task() (in module dammit.profile)
Profiler (class in dammit.profile)
R
raise_empty() (dammit.fileio.base.BaseParser method)
read() (dammit.fileio.base.ChunkParser method)
register_annotate_tasks() (in module dammit.annotate)
register_busco_task() (in module dammit.annotate)
register_busco_tasks() (in module dammit.databases)
register_lastal_tasks() (in module dammit.annotate)
register_nr_tasks() (in module dammit.databases)
register_orthodb_tasks() (in module dammit.databases)
register_pfam_tasks() (in module dammit.databases)
register_rfam_tasks() (in module dammit.annotate)
(in module dammit.databases)
register_stats_task() (in module dammit.annotate)
register_task() (dammit.handler.TaskHandler method)
register_transdecoder_tasks() (in module dammit.annotate)
register_uniref90_tasks() (in module dammit.databases)
register_user_db_tasks() (in module dammit.annotate)
run() (dammit.app.DammitApp method)
(dammit.handler.TaskHandler method)
run_annotation() (in module dammit.annotate)
S
setup_profiler() (in module dammit.profile)
shmlast_to_gff3() (in module dammit.fileio.gff3)
skip_ignore() (dammit.ui.GithubMarkdownReporter method)
skip_uptodate() (dammit.ui.GithubMarkdownReporter method)
start() (dammit.profile.Timer method)
start_logging() (in module dammit.log)
start_profiler() (dammit.profile.Profiler method)
StartProfiler() (in module dammit.profile)
stop() (dammit.profile.Timer method)
stop_profiler() (dammit.profile.Profiler method)
strip_seq_extension() (in module dammit.tasks.fastx)
T
task() (dammit.tasks.busco.BuscoTask method)
(dammit.tasks.hmmer.HMMPressTask method)
(dammit.tasks.hmmer.HMMScanTask method)
(dammit.tasks.infernal.CMPressTask method)
(dammit.tasks.infernal.CMScanTask method)
(dammit.tasks.transdecoder.TransDecoderLongOrfsTask method)
(dammit.tasks.transdecoder.TransDecoderPredictTask method)
(dammit.tasks.utils.DependentTask method)
TaskHandler (class in dammit.handler)
Timer (class in dammit.profile)
title() (dammit.utils.DammitTask method)
title_without_profile_actions() (in module dammit.profile)
touch() (in module dammit.utils)
TransDecoderLongOrfsTask (class in dammit.tasks.transdecoder)
TransDecoderPredictTask (class in dammit.tasks.transdecoder)
V
version_line (dammit.fileio.gff3.GFF3Writer attribute)
W
warn_empty() (in module dammit.fileio.base)
which() (in module dammit.utils)
write() (dammit.fileio.gff3.GFF3Writer method)
write_result() (dammit.profile.Profiler method)
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