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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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L
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M
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N
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P
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R
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S
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T
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V
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W
A
accounce_changes() (in module drep.d_adjust)
add_centrality() (in module drep.d_choose)
,
[1]
add_taxonomy() (in module drep.d_bonus)
adjust_cluster_wrapper() (in module drep.d_adjust)
C
calc_centrality_from_scratch() (in module drep.d_choose)
,
[1]
calc_dist() (in module drep.d_analyze)
,
[1]
calc_fasta_length() (in module drep.d_filter)
,
[1]
calc_genome_info() (in module drep.d_filter)
,
[1]
calc_n50() (in module drep.d_filter)
,
[1]
chdb_to_genomeInfo() (in module drep.d_filter)
,
[1]
check_dependencies() (in module drep.d_bonus)
choose_winners() (in module drep.d_choose)
,
[1]
clobber_dir() (in module drep)
cluster_test_wrapper() (in module drep.d_analyze)
,
[1]
cluster_type() (in module drep.d_adjust)
comp_str() (in module drep.d_evaluate)
compare_operation() (drep.controller.Controller method)
compare_winners() (in module drep.d_evaluate)
compare_wrapper() (in module drep.d_workflows)
con_str() (in module drep.d_evaluate)
Controller (class in drep.controller)
D
d_adjust_wrapper() (in module drep.d_adjust)
d_analyze_wrapper() (in module drep.d_analyze)
,
[1]
d_bonus_wrapper() (in module drep.d_bonus)
d_choose_wrapper() (in module drep.d_choose)
,
[1]
d_evaluate_wrapper() (in module drep.d_evaluate)
d_filter_wrapper() (in module drep.d_filter)
,
[1]
dereplicate_operation() (drep.controller.Controller method)
dereplicate_wrapper() (in module drep.d_workflows)
drep (module)
drep.argumentParser (module)
drep.controller (module)
drep.d_adjust (module)
drep.d_analyze (module)
,
[1]
drep.d_bonus (module)
drep.d_choose (module)
,
[1]
drep.d_cluster (module)
,
[1]
drep.d_evaluate (module)
drep.d_filter (module)
,
[1]
drep.d_workflows (module)
drep.WorkDirectory (module)
,
[1]
E
evaluate_warnings() (in module drep.d_evaluate)
evaluate_winners() (in module drep.d_evaluate)
F
fancy_dendrogram() (in module drep.d_analyze)
,
[1]
filter_bdb() (in module drep.d_filter)
,
[1]
find_program() (in module drep.d_bonus)
firstLevels (drep.WorkDirectory.WorkDirectory attribute)
,
[1]
G
gen_centrifuge_cmd() (in module drep.d_bonus)
gen_color_dictionary() (in module drep.d_analyze)
,
[1]
gen_color_list() (in module drep.d_analyze)
,
[1]
gen_phylo_db() (in module drep.d_bonus)
gen_read2bin() (in module drep.d_bonus)
get_cluster() (drep.WorkDirectory.WorkDirectory method)
,
[1]
get_db() (drep.WorkDirectory.WorkDirectory method)
,
[1]
get_dir() (drep.WorkDirectory.WorkDirectory method)
,
[1]
get_exe() (in module drep)
get_highest_self() (in module drep.d_analyze)
,
[1]
get_loc() (drep.WorkDirectory.WorkDirectory method)
,
[1]
get_primary_linkage() (drep.WorkDirectory.WorkDirectory method)
,
[1]
get_scaff() (in module drep.d_bonus)
H
hasDb() (drep.WorkDirectory.WorkDirectory method)
,
[1]
I
import_arguments() (drep.WorkDirectory.WorkDirectory method)
,
[1]
import_clusters() (drep.WorkDirectory.WorkDirectory method)
,
[1]
import_data_tables() (drep.WorkDirectory.WorkDirectory method)
,
[1]
L
lineage_from_taxId() (in module drep.d_bonus)
load_cached() (drep.WorkDirectory.WorkDirectory method)
,
[1]
load_extra_weight_table() (in module drep.d_choose)
,
[1]
loadDefaultArgs() (drep.controller.Controller method)
M
make_dir() (in module drep)
make_fileStructure() (drep.WorkDirectory.WorkDirectory method)
,
[1]
mash_dendrogram_from_wd() (in module drep.d_analyze)
,
[1]
N
normalize() (in module drep.d_analyze)
,
[1]
P
parse_args() (in module drep.argumentParser)
parse_centrifuge() (in module drep.d_bonus)
parse_centrifuge_percent() (in module drep.d_bonus)
parse_raw_centrifuge() (in module drep.d_bonus)
parse_taxonomy() (in module drep.d_bonus)
parseArguments() (drep.controller.Controller method)
pick_winners() (in module drep.d_choose)
,
[1]
plot_ANIn_vs_ANIn_cov() (in module drep.d_analyze)
,
[1]
plot_ANIn_vs_len() (in module drep.d_analyze)
,
[1]
plot_binscoring_from_wd() (in module drep.d_analyze)
,
[1]
plot_clustertest() (in module drep.d_analyze)
,
[1]
plot_MASH_dendrogram() (in module drep.d_analyze)
,
[1]
plot_MASH_vs_ANIn_ani() (in module drep.d_analyze)
,
[1]
plot_MASH_vs_ANIn_cov() (in module drep.d_analyze)
,
[1]
plot_MASH_vs_len() (in module drep.d_analyze)
,
[1]
plot_MASH_vs_secondary_ani() (in module drep.d_analyze)
,
[1]
plot_scatterplots() (in module drep.d_analyze)
,
[1]
plot_scatterplots_from_wd() (in module drep.d_analyze)
,
[1]
plot_secondary_dendrograms_from_wd() (in module drep.d_analyze)
,
[1]
plot_secondary_mds_from_wd() (in module drep.d_analyze)
,
[1]
plot_winner_scoring_complex() (in module drep.d_analyze)
,
[1]
plot_winners() (in module drep.d_analyze)
,
[1]
plot_winners_from_wd() (in module drep.d_analyze)
,
[1]
printHelp() (in module drep.argumentParser)
R
remove_cluster_wrapper() (in module drep.d_adjust)
remove_primary_cluster() (in module drep.d_adjust)
remove_secondary_cluster() (in module drep.d_adjust)
run_centrifuge() (in module drep.d_bonus)
run_checkM() (in module drep.d_filter)
,
[1]
run_cmd() (in module drep)
run_prodigal() (in module drep.d_filter)
,
[1]
run_taxonomy() (in module drep.d_bonus)
run_tertiary_clustering() (in module drep.d_evaluate)
S
sanity_check() (in module drep.d_filter)
,
[1]
score_genomes() (in module drep.d_choose)
,
[1]
score_row() (in module drep.d_choose)
,
[1]
setup_logger() (drep.controller.Controller method)
SmartFormatter (class in drep.argumentParser)
store_db() (drep.WorkDirectory.WorkDirectory method)
,
[1]
store_special() (drep.WorkDirectory.WorkDirectory method)
,
[1]
T
tdb_from_hits() (in module drep.d_bonus)
test_adjust() (in module drep.d_adjust)
thread_cmd_wrapper() (in module drep)
thread_cmds() (in module drep)
V
validate_arguments() (in module drep.d_bonus)
validate_chdb() (in module drep.d_filter)
,
[1]
validate_compare() (in module drep.d_workflows)
validate_dereplicate() (in module drep.d_workflows)
VERSION (in module drep.argumentParser)
version() (in module drep.argumentParser)
(in module drep.controller)
W
WorkDirectory (class in drep.WorkDirectory)
,
[1]
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