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A
accession (pyani.scripts.subcommands.subcmd_download.Skipped attribute)
add_alignment() (pyani.nucmer.DeltaComparison method)
add_colorbar() (in module pyani.pyani_graphics.mpl)
add_colorscale() (in module pyani.pyani_graphics.mpl)
add_coverage() (pyani.pyani_tools.ANIResults method)
add_dendrogram() (in module pyani.pyani_graphics.mpl)
add_dependency() (pyani.pyani_jobs.Job method)
(pyani.pyani_jobs.JobGroup method)
add_labels() (in module pyani.pyani_graphics.mpl)
(in module pyani.pyani_graphics.sns)
add_log_headers() (in module pyani.scripts.pyani_script)
add_pid() (pyani.pyani_tools.ANIResults method)
add_run() (in module pyani.pyani_orm)
add_run_genomes() (in module pyani.pyani_orm)
add_sim_errors() (pyani.pyani_tools.ANIResults method)
add_tot_length() (pyani.pyani_tools.ANIResults method)
all_components_k_complete() (in module pyani.pyani_classify)
all_k_complete (pyani.pyani_classify.Cliquesinfo attribute)
aln_length (pyani.pyani_orm.Comparison attribute)
(pyani.scripts.subcommands.subcmd_anim.ComparisonResult attribute)
(pyani.scripts.subcommands.subcmd_fastani.ComparisonResult attribute)
analyse_cliques() (in module pyani.pyani_classify)
ani (pyani.fastani.ComparisonResult attribute)
ANIResults (class in pyani.pyani_tools)
ANSI_RE (pyani.logger.NoColorFormatter attribute)
asm_ids (pyani.download.ASMIDs attribute)
ASMIDs (class in pyani.download)
B
blast (pyani.pyani_tools.Dependencies attribute)
blast_exe (pyani.pyani_tools.BLASTexes attribute)
BLASTcmds (class in pyani.pyani_tools)
BlastDB (class in pyani.pyani_orm)
blastdb_id (pyani.pyani_orm.BlastDB attribute)
blastdbs (pyani.pyani_orm.Genome attribute)
(pyani.pyani_orm.Run attribute)
BLASTexes (class in pyani.pyani_tools)
BLASTfunctions (class in pyani.pyani_tools)
blastn_func (pyani.pyani_tools.BLASTfunctions attribute)
build() (in module pyani.scripts.parsers.anib_parser)
(in module pyani.scripts.parsers.aniblastall_parser)
(in module pyani.scripts.parsers.anim_parser)
(in module pyani.scripts.parsers.classify_parser)
(in module pyani.scripts.parsers.common_parser)
(in module pyani.scripts.parsers.createdb_parser)
(in module pyani.scripts.parsers.download_parser)
(in module pyani.scripts.parsers.fastani_parser)
(in module pyani.scripts.parsers.index_parser)
(in module pyani.scripts.parsers.listdeps_parser)
(in module pyani.scripts.parsers.plot_parser)
(in module pyani.scripts.parsers.report_parser)
(in module pyani.scripts.parsers.run_common_parser)
(in module pyani.scripts.parsers.scheduling_parser)
build_and_submit_jobs() (in module pyani.run_sge)
build_blast_cmd() (pyani.pyani_tools.BLASTcmds method)
build_db_cmd() (pyani.pyani_tools.BLASTcmds method)
build_db_jobs() (in module pyani.anib)
build_directories() (in module pyani.run_sge)
build_graph_from_results() (in module pyani.pyani_classify)
build_job_scripts() (in module pyani.run_sge)
build_joblist() (in module pyani.run_sge)
C
calculate_anim() (in module pyani.scripts.average_nucleotide_identity)
calculate_correlations() (in module pyani.tetra)
calculate_tetra() (in module pyani.scripts.average_nucleotide_identity)
calculate_tetra_zscore() (in module pyani.tetra)
calculate_tetra_zscores() (in module pyani.tetra)
check_hash() (in module pyani.download)
class_label (pyani.pyani_orm.Label attribute)
(pyani.pyani_orm.LabelTuple attribute)
Classification (class in pyani.download)
clean_axis() (in module pyani.pyani_graphics.mpl)
cliqueinfo (pyani.scripts.subcommands.subcmd_classify.SubgraphData attribute)
Cliquesinfo (class in pyani.pyani_classify)
cmdline (pyani.pyani_orm.Run attribute)
(pyani.scripts.subcommands.subcmd_anim.RunData attribute)
(pyani.scripts.subcommands.subcmd_fastani.RunData attribute)
collect_existing_output() (in module pyani.pyani_files)
colour_coverage() (in module pyani.pyani_report)
colour_identity() (in module pyani.pyani_report)
colour_numeric() (in module pyani.pyani_report)
colour_rows() (in module pyani.pyani_report)
Comparison (class in pyani.pyani_orm)
comparison_id (pyani.pyani_orm.Comparison attribute)
ComparisonJob (class in pyani.scripts.subcommands.subcmd_anim)
(class in pyani.scripts.subcommands.subcmd_fastani)
ComparisonResult (class in pyani.fastani)
(class in pyani.scripts.subcommands.subcmd_anim)
(class in pyani.scripts.subcommands.subcmd_fastani)
comparisons (pyani.nucmer.DeltaData attribute)
(pyani.pyani_orm.Run attribute)
compile_jobgroups_from_joblist() (in module pyani.run_sge)
compile_url() (in module pyani.download)
compress_delete_outdir() (in module pyani.scripts.average_nucleotide_identity)
config_logger() (in module pyani.logger)
configure_entrez() (in module pyani.scripts.subcommands.subcmd_download)
construct_blastall_cmdline() (in module pyani.anib)
construct_blastn_cmdline() (in module pyani.anib)
construct_fastani_cmdline() (in module pyani.fastani)
construct_formatdb_cmd() (in module pyani.anib)
construct_makeblastdb_cmd() (in module pyani.anib)
construct_nucmer_cmdline() (in module pyani.anim)
construct_output_paths() (in module pyani.download)
cov_query (pyani.pyani_orm.Comparison attribute)
cov_subject (pyani.pyani_orm.Comparison attribute)
create_db() (in module pyani.pyani_orm)
create_hash() (in module pyani.download)
create_labels() (in module pyani.download)
D
data (pyani.pyani_tools.ANIResults attribute)
(pyani.pyani_tools.MatrixData attribute)
date (pyani.pyani_orm.Run attribute)
(pyani.scripts.subcommands.subcmd_anim.RunData attribute)
(pyani.scripts.subcommands.subcmd_fastani.RunData attribute)
db_func (pyani.pyani_tools.BLASTfunctions attribute)
dbcmd (pyani.pyani_orm.BlastDB attribute)
dbpath (pyani.pyani_orm.BlastDB attribute)
DeltaAlignment (class in pyani.nucmer)
DeltaComparison (class in pyani.nucmer)
DeltaData (class in pyani.nucmer)
DeltaHeader (class in pyani.nucmer)
DeltaIterator (class in pyani.nucmer)
DeltaMetadata (class in pyani.nucmer)
Dependencies (class in pyani.pyani_tools)
description (pyani.pyani_orm.Genome attribute)
df_alnlength (pyani.pyani_orm.Run attribute)
df_coverage (pyani.pyani_orm.Run attribute)
df_hadamard (pyani.pyani_orm.Run attribute)
df_identity (pyani.pyani_orm.Run attribute)
df_simerrors (pyani.pyani_orm.Run attribute)
distribution() (in module pyani.pyani_graphics.mpl)
(in module pyani.pyani_graphics.sns)
dl_info_to_str() (in module pyani.scripts.subcommands.subcmd_download)
DLFileData (class in pyani.download)
DLStatus (class in pyani.download)
dltype (pyani.scripts.subcommands.subcmd_download.Skipped attribute)
download_data() (in module pyani.scripts.subcommands.subcmd_download)
download_genome() (in module pyani.scripts.subcommands.subcmd_download)
download_genome_and_hash() (in module pyani.download)
download_url() (in module pyani.download)
draw() (in module pyani.scripts.average_nucleotide_identity)
E
entrez_batch() (in module pyani.download)
entrez_batch_webhistory() (in module pyani.scripts.genbank_get_genomes_by_taxon)
entrez_batched_webhistory() (in module pyani.download)
entrez_esearch() (in module pyani.download)
entrez_esummary() (in module pyani.download)
entrez_retry() (in module pyani.download)
(in module pyani.scripts.genbank_get_genomes_by_taxon)
extract_archive() (in module pyani.scripts.genbank_get_genomes_by_taxon)
extract_contigs() (in module pyani.download)
extract_filestem() (in module pyani.download)
(in module pyani.scripts.genbank_get_genomes_by_taxon)
extract_genomes() (in module pyani.scripts.subcommands.subcmd_download)
extract_hash() (in module pyani.download)
extract_submittable_jobs() (in module pyani.run_sge)
F
fastcmd (pyani.scripts.subcommands.subcmd_fastani.ComparisonJob attribute)
FileExistsException
filehash (pyani.download.Hashstatus attribute)
filestem (pyani.download.DLFileData attribute)
filter_existing_comparisons() (in module pyani.pyani_orm)
filtercmd (pyani.scripts.subcommands.subcmd_anim.ComparisonJob attribute)
format() (pyani.logger.NoColorFormatter method)
format_exe (pyani.pyani_tools.BLASTexes attribute)
fragLen (pyani.scripts.subcommands.subcmd_fastani.ComparisonJob attribute)
fragment_fasta_file() (in module pyani.scripts.subcommands.subcmd_anib)
fragment_fasta_files() (in module pyani.anib)
fragments (pyani.fastani.ComparisonResult attribute)
fragpath (pyani.pyani_orm.BlastDB attribute)
fragsize (pyani.pyani_orm.Comparison attribute)
(pyani.scripts.subcommands.subcmd_anim.ProgParams attribute)
fragsizes (pyani.pyani_orm.BlastDB attribute)
from_delta() (pyani.nucmer.DeltaData method)
ftpstem (pyani.download.DLFileData attribute)
G
generate_blastdb_commands() (in module pyani.anib)
generate_blastn_commands() (in module pyani.anib)
generate_fastani_commands() (in module pyani.fastani)
generate_fastani_jobs() (in module pyani.fastani)
generate_joblist() (in module pyani.scripts.subcommands.subcmd_anib)
(in module pyani.scripts.subcommands.subcmd_anim)
(in module pyani.scripts.subcommands.subcmd_fastani)
generate_nucmer_commands() (in module pyani.anim)
generate_nucmer_jobs() (in module pyani.anim)
generate_script() (pyani.pyani_jobs.JobGroup method)
Genome (class in pyani.pyani_orm)
genome (pyani.pyani_orm.BlastDB attribute)
(pyani.pyani_orm.Label attribute)
genome_hash (pyani.pyani_orm.Genome attribute)
genome_id (pyani.pyani_orm.BlastDB attribute)
(pyani.pyani_orm.Genome attribute)
(pyani.pyani_orm.Label attribute)
genomes (pyani.pyani_orm.Run attribute)
genus (pyani.download.Classification attribute)
get_asm_uids() (in module pyani.download)
(in module pyani.scripts.genbank_get_genomes_by_taxon)
get_clustermap() (in module pyani.pyani_graphics.sns)
get_colorbar() (in module pyani.pyani_graphics.sns)
get_colormap() (in module pyani.pyani_config)
get_comparison_dict() (in module pyani.pyani_orm)
get_db_name() (pyani.pyani_tools.BLASTcmds method)
get_dev_requirements() (in module pyani.dependencies)
get_fasta_and_hash_paths() (in module pyani.pyani_files)
get_fasta_files() (in module pyani.anim)
(in module pyani.pyani_files)
get_fasta_paths() (in module pyani.pyani_files)
get_fraglength_dict() (in module pyani.anib)
get_fragment_lengths() (in module pyani.anib)
get_genome_length() (in module pyani.pyani_tools)
get_heatmap_axes() (in module pyani.pyani_graphics.mpl)
get_input_files() (in module pyani.pyani_files)
get_labels() (in module pyani.pyani_tools)
get_matrix_classes_for_run() (in module pyani.pyani_orm)
get_matrix_labels_for_run() (in module pyani.pyani_orm)
get_method() (in module pyani.scripts.average_nucleotide_identity)
get_ncbi_asm() (in module pyani.scripts.genbank_get_genomes_by_taxon)
get_ncbi_classification() (in module pyani.download)
get_ncbi_esummary() (in module pyani.download)
get_pip_requirements() (in module pyani.dependencies)
get_requirements() (in module pyani.dependencies)
get_sequence_lengths() (in module pyani.pyani_files)
get_session() (in module pyani.pyani_orm)
get_tax_asm_dict() (in module pyani.scripts.subcommands.subcmd_download)
get_tool_versions() (in module pyani.dependencies)
get_version() (in module pyani.anib)
(in module pyani.aniblastall)
(in module pyani.anim)
(in module pyani.fastani)
get_versions() (in module pyani.dependencies)
graph (pyani.scripts.subcommands.subcmd_classify.SubgraphData attribute)
graphic_args (pyani.pyani_tools.MatrixData attribute)
H
hadamard (pyani.pyani_tools.ANIResults attribute)
has_dependencies() (in module pyani.pyani_tools)
hash_genomes() (in module pyani.scripts.subcommands.subcmd_download)
Hashstatus (class in pyani.download)
header_font() (in module pyani.pyani_report)
headers (pyani.scripts.subcommands.subcmd_report.ReportParams attribute)
heatmap() (in module pyani.pyani_graphics.mpl)
(in module pyani.pyani_graphics.sns)
hover_highlight() (in module pyani.pyani_report)
I
identity (pyani.pyani_orm.Comparison attribute)
interval (pyani.scripts.subcommands.subcmd_classify.SubgraphData attribute)
J
Job (class in pyani.pyani_jobs)
job (pyani.scripts.subcommands.subcmd_anim.ComparisonJob attribute)
(pyani.scripts.subcommands.subcmd_fastani.ComparisonJob attribute)
JobGroup (class in pyani.pyani_jobs)
K
k_complete_component_status() (in module pyani.pyani_classify)
kmersize (pyani.pyani_orm.Comparison attribute)
kmerSize (pyani.scripts.subcommands.subcmd_fastani.ComparisonJob attribute)
L
Label (class in pyani.pyani_orm)
label (pyani.pyani_orm.Label attribute)
(pyani.pyani_orm.LabelTuple attribute)
label_id (pyani.pyani_orm.Label attribute)
label_results_matrix() (in module pyani.pyani_tools)
labels (pyani.pyani_orm.Genome attribute)
(pyani.pyani_orm.Run attribute)
LabelTuple (class in pyani.pyani_orm)
last_exception() (in module pyani.download)
(in module pyani.scripts.average_nucleotide_identity)
(in module pyani.scripts.genbank_get_genomes_by_taxon)
legacy_blast (pyani.pyani_tools.Dependencies attribute)
length (pyani.pyani_orm.Genome attribute)
load_classes_labels() (in module pyani.pyani_files)
localhash (pyani.download.Hashstatus attribute)
logreport_downloaded() (in module pyani.scripts.genbank_get_genomes_by_taxon)
M
make_asm_dict() (in module pyani.download)
make_blastcmd_builder() (in module pyani.anib)
make_job_graph() (in module pyani.anib)
make_outdir() (in module pyani.scripts)
(in module pyani.scripts.genbank_get_genomes_by_taxon)
make_outdirs() (in module pyani.scripts.average_nucleotide_identity)
make_sequence_fragments() (in module pyani.scripts.average_nucleotide_identity)
matches (pyani.fastani.ComparisonResult attribute)
MatrixData (class in pyani.pyani_tools)
maxmatch (pyani.pyani_orm.Comparison attribute)
(pyani.scripts.subcommands.subcmd_anim.ProgParams attribute)
metadata (pyani.nucmer.DeltaData attribute)
method (pyani.pyani_orm.Run attribute)
(pyani.scripts.subcommands.subcmd_anim.RunData attribute)
(pyani.scripts.subcommands.subcmd_fastani.RunData attribute)
minFraction (pyani.scripts.subcommands.subcmd_fastani.ComparisonJob attribute)
minmatch (pyani.pyani_orm.Comparison attribute)
multiprocessing_run() (in module pyani.run_multiprocessing)
mummer (pyani.pyani_tools.Dependencies attribute)
N
n_nodes (pyani.pyani_classify.Cliquesinfo attribute)
n_subgraphs (pyani.pyani_classify.Cliquesinfo attribute)
name (pyani.pyani_orm.Run attribute)
(pyani.pyani_tools.MatrixData attribute)
(pyani.scripts.subcommands.subcmd_anim.RunData attribute)
(pyani.scripts.subcommands.subcmd_fastani.RunData attribute)
(pyani.scripts.subcommands.subcmd_report.ReportParams attribute)
NCBIDownloadException
,
[1]
NoColorFormatter (class in pyani.logger)
nucmercmd (pyani.scripts.subcommands.subcmd_anim.ComparisonJob attribute)
O
organism (pyani.download.Classification attribute)
(pyani.scripts.subcommands.subcmd_download.Skipped attribute)
outfile (pyani.scripts.subcommands.subcmd_anim.ComparisonJob attribute)
(pyani.scripts.subcommands.subcmd_fastani.ComparisonJob attribute)
P
Params (class in pyani.pyani_graphics)
params_mpl() (in module pyani.pyani_config)
parse_api_key() (in module pyani.scripts.subcommands.subcmd_download)
parse_blast_tab() (in module pyani.anib)
parse_blasttab() (in module pyani.blast)
parse_cmdline() (in module pyani.scripts.average_nucleotide_identity)
(in module pyani.scripts.genbank_get_genomes_by_taxon)
(in module pyani.scripts.parsers)
parse_delta() (in module pyani.anim)
parse_fastani_file() (in module pyani.fastani)
passed (pyani.download.Hashstatus attribute)
path (pyani.pyani_orm.Genome attribute)
pid (pyani.scripts.subcommands.subcmd_anim.ComparisonResult attribute)
(pyani.scripts.subcommands.subcmd_fastani.ComparisonResult attribute)
populate_cmdsets() (in module pyani.run_multiprocessing)
populate_jobset() (in module pyani.run_sge)
process_arguments() (in module pyani.scripts.average_nucleotide_identity)
process_blast() (in module pyani.anib)
process_deltadir() (in module pyani.anim)
process_files() (in module pyani.fastani)
process_formats() (in module pyani.scripts.subcommands.subcmd_report)
ProgData (class in pyani.scripts.subcommands.subcmd_anim)
ProgParams (class in pyani.scripts.subcommands.subcmd_anim)
program (pyani.nucmer.DeltaData attribute)
(pyani.pyani_orm.Comparison attribute)
(pyani.scripts.subcommands.subcmd_anim.ProgData attribute)
pyani (module)
pyani.anib (module)
pyani.aniblastall (module)
pyani.anim (module)
pyani.blast (module)
pyani.dependencies (module)
pyani.download (module)
pyani.fastani (module)
pyani.logger (module)
pyani.nucmer (module)
pyani.pyani_classify (module)
pyani.pyani_config (module)
pyani.pyani_files (module)
pyani.pyani_graphics (module)
pyani.pyani_graphics.mpl (module)
pyani.pyani_graphics.sns (module)
pyani.pyani_jobs (module)
pyani.pyani_orm (module)
pyani.pyani_report (module)
pyani.pyani_tools (module)
pyani.run_multiprocessing (module)
pyani.run_sge (module)
pyani.scripts (module)
pyani.scripts.average_nucleotide_identity (module)
pyani.scripts.delta_filter_wrapper (module)
pyani.scripts.genbank_get_genomes_by_taxon (module)
pyani.scripts.parsers (module)
pyani.scripts.parsers.anib_parser (module)
pyani.scripts.parsers.aniblastall_parser (module)
pyani.scripts.parsers.anim_parser (module)
pyani.scripts.parsers.classify_parser (module)
pyani.scripts.parsers.common_parser (module)
pyani.scripts.parsers.createdb_parser (module)
pyani.scripts.parsers.download_parser (module)
pyani.scripts.parsers.fastani_parser (module)
pyani.scripts.parsers.index_parser (module)
pyani.scripts.parsers.listdeps_parser (module)
pyani.scripts.parsers.plot_parser (module)
pyani.scripts.parsers.report_parser (module)
pyani.scripts.parsers.run_common_parser (module)
pyani.scripts.parsers.scheduling_parser (module)
pyani.scripts.pyani_script (module)
pyani.scripts.subcommands (module)
pyani.scripts.subcommands.subcmd_anib (module)
pyani.scripts.subcommands.subcmd_aniblastall (module)
pyani.scripts.subcommands.subcmd_anim (module)
pyani.scripts.subcommands.subcmd_classify (module)
pyani.scripts.subcommands.subcmd_createdb (module)
pyani.scripts.subcommands.subcmd_download (module)
pyani.scripts.subcommands.subcmd_fastani (module)
pyani.scripts.subcommands.subcmd_index (module)
pyani.scripts.subcommands.subcmd_listdeps (module)
pyani.scripts.subcommands.subcmd_plot (module)
pyani.scripts.subcommands.subcmd_report (module)
pyani.tetra (module)
PyaniANIbException
PyaniANImException
PyaniblastallException
PyaniException
PyaniFastANIException
PyaniFilesException
PyaniIndexException
PyaniORMException
PyaniScriptException
Q
qcov (pyani.scripts.subcommands.subcmd_anim.ComparisonResult attribute)
(pyani.scripts.subcommands.subcmd_fastani.ComparisonResult attribute)
qid (pyani.scripts.subcommands.subcmd_anim.ComparisonResult attribute)
(pyani.scripts.subcommands.subcmd_fastani.ComparisonResult attribute)
qlen (pyani.scripts.subcommands.subcmd_anim.ComparisonResult attribute)
(pyani.scripts.subcommands.subcmd_fastani.ComparisonResult attribute)
query (pyani.download.ASMIDs attribute)
(pyani.fastani.ComparisonResult attribute)
(pyani.nucmer.DeltaData attribute)
(pyani.pyani_orm.Comparison attribute)
(pyani.scripts.subcommands.subcmd_anim.ComparisonJob attribute)
(pyani.scripts.subcommands.subcmd_fastani.ComparisonJob attribute)
query_comparisons (pyani.pyani_orm.Genome attribute)
query_id (pyani.pyani_orm.Comparison attribute)
R
rcov (pyani.scripts.subcommands.subcmd_fastani.ComparisonResult attribute)
read_fasta_description() (in module pyani.pyani_files)
read_hash_string() (in module pyani.pyani_files)
ref (pyani.scripts.subcommands.subcmd_fastani.ComparisonJob attribute)
reference (pyani.fastani.ComparisonResult attribute)
(pyani.nucmer.DeltaData attribute)
remove_dependency() (pyani.pyani_jobs.Job method)
(pyani.pyani_jobs.JobGroup method)
remove_low_weight_edges() (in module pyani.pyani_classify)
report() (in module pyani.scripts.subcommands.subcmd_report)
ReportParams (class in pyani.scripts.subcommands.subcmd_report)
result_count (pyani.download.ASMIDs attribute)
retrieve_asm_contigs() (in module pyani.scripts.genbank_get_genomes_by_taxon)
retrieve_genome_and_hash() (in module pyani.download)
rid (pyani.scripts.subcommands.subcmd_fastani.ComparisonResult attribute)
rlen (pyani.scripts.subcommands.subcmd_fastani.ComparisonResult attribute)
Run (class in pyani.pyani_orm)
run (pyani.pyani_orm.BlastDB attribute)
(pyani.pyani_orm.Label attribute)
run_anim_jobs() (in module pyani.scripts.subcommands.subcmd_anim)
run_blast() (in module pyani.scripts.average_nucleotide_identity)
run_dependency_graph() (in module pyani.run_multiprocessing)
(in module pyani.run_sge)
run_fastani_jobs() (in module pyani.scripts.subcommands.subcmd_fastani)
run_id (pyani.pyani_orm.BlastDB attribute)
(pyani.pyani_orm.Label attribute)
(pyani.pyani_orm.Run attribute)
run_main() (in module pyani.scripts.average_nucleotide_identity)
(in module pyani.scripts.delta_filter_wrapper)
(in module pyani.scripts.genbank_get_genomes_by_taxon)
(in module pyani.scripts.pyani_script)
RunData (class in pyani.scripts.subcommands.subcmd_anim)
(class in pyani.scripts.subcommands.subcmd_fastani)
runs (pyani.pyani_orm.Comparison attribute)
(pyani.pyani_orm.Genome attribute)
S
scatter() (in module pyani.pyani_graphics.mpl)
(in module pyani.pyani_graphics.sns)
scov (pyani.scripts.subcommands.subcmd_anim.ComparisonResult attribute)
set_ncbi_email() (in module pyani.download)
(in module pyani.scripts.genbank_get_genomes_by_taxon)
sid (pyani.scripts.subcommands.subcmd_anim.ComparisonResult attribute)
sim_errs (pyani.pyani_orm.Comparison attribute)
(pyani.scripts.subcommands.subcmd_anim.ComparisonResult attribute)
(pyani.scripts.subcommands.subcmd_fastani.ComparisonResult attribute)
Skipped (class in pyani.scripts.subcommands.subcmd_download)
slen (pyani.scripts.subcommands.subcmd_anim.ComparisonResult attribute)
species (pyani.download.Classification attribute)
split_seq() (in module pyani.run_sge)
split_taxa() (in module pyani.download)
statement (pyani.scripts.subcommands.subcmd_report.ReportParams attribute)
status (pyani.pyani_orm.Run attribute)
strain (pyani.download.Classification attribute)
(pyani.scripts.subcommands.subcmd_download.Skipped attribute)
subcmd_anib() (in module pyani.scripts.subcommands.subcmd_anib)
subcmd_aniblastall() (in module pyani.scripts.subcommands.subcmd_aniblastall)
subcmd_anim() (in module pyani.scripts.subcommands.subcmd_anim)
subcmd_classify() (in module pyani.scripts.subcommands.subcmd_classify)
subcmd_createdb() (in module pyani.scripts.subcommands.subcmd_createdb)
subcmd_download() (in module pyani.scripts.subcommands.subcmd_download)
subcmd_fastani() (in module pyani.scripts.subcommands.subcmd_fastani)
subcmd_index() (in module pyani.scripts.subcommands.subcmd_index)
subcmd_listdeps() (in module pyani.scripts.subcommands.subcmd_listdeps)
subcmd_plot() (in module pyani.scripts.subcommands.subcmd_plot)
subcmd_report() (in module pyani.scripts.subcommands.subcmd_report)
SubgraphData (class in pyani.scripts.subcommands.subcmd_classify)
subject (pyani.pyani_orm.Comparison attribute)
(pyani.scripts.subcommands.subcmd_anim.ComparisonJob attribute)
subject_comparisons (pyani.pyani_orm.Genome attribute)
subject_id (pyani.pyani_orm.Comparison attribute)
submit_jobs() (in module pyani.run_sge)
submit_safe_jobs() (in module pyani.run_sge)
subsample_input() (in module pyani.scripts.average_nucleotide_identity)
suffix (pyani.download.DLFileData attribute)
T
table_padding() (in module pyani.pyani_report)
taxon_id (pyani.scripts.subcommands.subcmd_download.Skipped attribute)
termcolor() (in module pyani.pyani_tools)
test_class_label_paths() (in module pyani.scripts.average_nucleotide_identity)
test_scheduler() (in module pyani.scripts.average_nucleotide_identity)
tetra_clean() (in module pyani.tetra)
trimmed_graph_sequence() (in module pyani.scripts.subcommands.subcmd_classify)
U
unified_anib() (in module pyani.scripts.average_nucleotide_identity)
update_comparison_matrices() (in module pyani.pyani_orm)
update_comparison_results() (in module pyani.scripts.subcommands.subcmd_anim)
(in module pyani.scripts.subcommands.subcmd_fastani)
url (pyani.scripts.subcommands.subcmd_download.Skipped attribute)
V
vdiff (pyani.pyani_graphics.Params attribute)
version (pyani.pyani_orm.Comparison attribute)
(pyani.scripts.subcommands.subcmd_anim.ProgData attribute)
W
wait() (pyani.pyani_jobs.Job method)
(pyani.pyani_jobs.JobGroup method)
write() (in module pyani.scripts.average_nucleotide_identity)
write_contigs() (in module pyani.scripts.genbank_get_genomes_by_taxon)
write_dbtable() (in module pyani.pyani_report)
write_distribution() (in module pyani.scripts.subcommands.subcmd_plot)
write_heatmap() (in module pyani.scripts.subcommands.subcmd_plot)
write_run_plots() (in module pyani.scripts.subcommands.subcmd_plot)
write_scatter() (in module pyani.scripts.subcommands.subcmd_plot)
write_styled_html() (in module pyani.pyani_report)
write_to_stdout() (in module pyani.pyani_report)
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