SYMBOL INDEX (370 symbols across 56 files)

FILE: docs/conf.py
  function run_apidoc (line 185) | def run_apidoc(_):
  function setup (line 193) | def setup(app):

FILE: pyani/__init__.py
  class PyaniException (line 46) | class PyaniException(Exception):

FILE: pyani/anib.py
  class PyaniANIbException (line 105) | class PyaniANIbException(PyaniException):
  function get_version (line 109) | def get_version(blast_exe: Path = pyani_config.BLASTN_DEFAULT) -> str:
  function fragment_fasta_files (line 164) | def fragment_fasta_files(
  function get_fraglength_dict (line 207) | def get_fraglength_dict(fastafiles: List[Path]) -> Dict:
  function get_fragment_lengths (line 224) | def get_fragment_lengths(fastafile: Path) -> Dict:
  function build_db_jobs (line 241) | def build_db_jobs(infiles: List[Path], blastcmds: BLASTcmds) -> Dict:
  function make_blastcmd_builder (line 257) | def make_blastcmd_builder(
  function make_job_graph (line 296) | def make_job_graph(
  function generate_blastdb_commands (line 351) | def generate_blastdb_commands(
  function construct_makeblastdb_cmd (line 378) | def construct_makeblastdb_cmd(
  function construct_formatdb_cmd (line 395) | def construct_formatdb_cmd(
  function generate_blastn_commands (line 410) | def generate_blastn_commands(
  function construct_blastn_cmdline (line 451) | def construct_blastn_cmdline(
  function construct_blastall_cmdline (line 475) | def construct_blastall_cmdline(
  function process_blast (line 496) | def process_blast(
  function parse_blast_tab (line 569) | def parse_blast_tab(

FILE: pyani/aniblastall.py
  class PyaniblastallException (line 51) | class PyaniblastallException(PyaniException):
  function get_version (line 56) | def get_version(blast_exe: Path = pyani_config.BLASTALL_DEFAULT) -> str:

FILE: pyani/anim.py
  class PyaniANImException (line 77) | class PyaniANImException(PyaniException):
  function get_fasta_files (line 82) | def get_fasta_files(dirname: Path = Path(".")) -> Iterable:
  function get_version (line 94) | def get_version(nucmer_exe: Path = pyani_config.NUCMER_DEFAULT) -> str:
  function generate_nucmer_jobs (line 155) | def generate_nucmer_jobs(
  function generate_nucmer_commands (line 192) | def generate_nucmer_commands(
  function construct_nucmer_cmdline (line 240) | def construct_nucmer_cmdline(
  function parse_delta (line 292) | def parse_delta(filename: Path) -> Tuple[int, int, float, int]:
  function process_deltadir (line 415) | def process_deltadir(

FILE: pyani/blast.py
  function parse_blasttab (line 44) | def parse_blasttab(fhandle: TextIO) -> List[List[str]]:

FILE: pyani/dependencies.py
  function get_versions (line 82) | def get_versions(deplist: str) -> Generator:
  function get_requirements (line 96) | def get_requirements() -> Generator:
  function get_dev_requirements (line 101) | def get_dev_requirements() -> Generator:
  function get_pip_requirements (line 106) | def get_pip_requirements() -> Generator:
  function get_tool_versions (line 111) | def get_tool_versions() -> Generator:

FILE: pyani/download.py
  class NCBIDownloadException (line 68) | class NCBIDownloadException(Exception):
    method __init__ (line 71) | def __init__(self, msg: str = "Error downloading file from NCBI"):
  class FileExistsException (line 76) | class FileExistsException(Exception):
    method __init__ (line 79) | def __init__(self, msg: str = "Specified file exists"):
  class PyaniIndexException (line 84) | class PyaniIndexException(Exception):
  class ASMIDs (line 88) | class ASMIDs(NamedTuple):
  class Classification (line 96) | class Classification(NamedTuple):
  class DLFileData (line 105) | class DLFileData(NamedTuple):
  class Hashstatus (line 113) | class Hashstatus(NamedTuple):
  class DLStatus (line 121) | class DLStatus:
    method __init__ (line 124) | def __init__(
  function last_exception (line 141) | def last_exception() -> str:
  function make_asm_dict (line 147) | def make_asm_dict(taxon_ids: List[str], retries: int) -> Dict:
  function set_ncbi_email (line 165) | def set_ncbi_email(email: str) -> None:
  function download_genome_and_hash (line 174) | def download_genome_and_hash(
  function entrez_retry (line 216) | def entrez_retry(func):
  function entrez_batch (line 234) | def entrez_batch(func):
  function entrez_batched_webhistory (line 255) | def entrez_batched_webhistory(*args, **kwargs):
  function entrez_esearch (line 260) | def entrez_esearch(*args, **kwargs):
  function entrez_esummary (line 265) | def entrez_esummary(*args, **kwargs):
  function split_taxa (line 270) | def split_taxa(taxa: str) -> List[str]:
  function get_asm_uids (line 286) | def get_asm_uids(taxon_uid: str, retries: int) -> ASMIDs:
  function extract_filestem (line 321) | def extract_filestem(esummary) -> str:
  function get_ncbi_esummary (line 339) | def get_ncbi_esummary(asm_uid, retries, api_key=None) -> Tuple:
  function get_ncbi_classification (line 375) | def get_ncbi_classification(esummary) -> Classification:
  function compile_url (line 393) | def compile_url(filestem: str, suffix: str, ftpstem: str) -> Tuple[str, ...
  function download_url (line 431) | def download_url(
  function construct_output_paths (line 466) | def construct_output_paths(
  function retrieve_genome_and_hash (line 481) | def retrieve_genome_and_hash(
  function check_hash (line 518) | def check_hash(fname: Path, hashfile: Path) -> Hashstatus:
  function extract_contigs (line 541) | def extract_contigs(fname: Path, ename: Path) -> CompletedProcess:
  function create_labels (line 555) | def create_labels(
  function create_hash (line 585) | def create_hash(fname: Path) -> str:
  function extract_hash (line 609) | def extract_hash(hashfile: Path, name: str) -> str:

FILE: pyani/fastani.py
  class PyaniFastANIException (line 55) | class PyaniFastANIException(PyaniException):
  class ComparisonResult (line 59) | class ComparisonResult(NamedTuple):
  function get_version (line 69) | def get_version(fastani_exe: Path = pyani_config.FASTANI_DEFAULT) -> str:
  function generate_fastani_jobs (line 126) | def generate_fastani_jobs(
  function generate_fastani_commands (line 158) | def generate_fastani_commands(
  function construct_fastani_cmdline (line 193) | def construct_fastani_cmdline(
  function parse_fastani_file (line 231) | def parse_fastani_file(filename: Path) -> ComparisonResult:
  function process_files (line 272) | def process_files(outdir: Path, org_lengths: Dict) -> ANIResults:

FILE: pyani/logger.py
  class NoColorFormatter (line 52) | class NoColorFormatter(logging.Formatter):
    method format (line 57) | def format(self, record):
  function config_logger (line 70) | def config_logger(args: Optional[Namespace] = None) -> None:

FILE: pyani/nucmer.py
  class DeltaData (line 47) | class DeltaData:
    method __init__ (line 68) | def __init__(self, name: str, handle: TextIO = None) -> None:
    method from_delta (line 80) | def from_delta(self, handle: TextIO) -> None:
    method comparisons (line 90) | def comparisons(self):
    method metadata (line 95) | def metadata(self):
    method reference (line 100) | def reference(self):
    method program (line 105) | def program(self):
    method query (line 110) | def query(self):
    method __eq__ (line 114) | def __eq__(self, other):
    method __len__ (line 124) | def __len__(self):
    method __str__ (line 127) | def __str__(self):
  class DeltaHeader (line 135) | class DeltaHeader:
    method __init__ (line 139) | def __init__(
    method __eq__ (line 154) | def __eq__(self, other):
    method __str__ (line 164) | def __str__(self):
  class DeltaAlignment (line 170) | class DeltaAlignment:
    method __init__ (line 174) | def __init__(
    method __lt__ (line 203) | def __lt__(self, other):
    method __eq__ (line 211) | def __eq__(self, other):
    method __str__ (line 219) | def __str__(self):
  class DeltaMetadata (line 234) | class DeltaMetadata:
    method __init__ (line 238) | def __init__(self) -> None:
    method __eq__ (line 244) | def __eq__(self, other):
    method __str__ (line 253) | def __str__(self):
  class DeltaComparison (line 257) | class DeltaComparison:
    method __init__ (line 261) | def __init__(self, header: DeltaHeader, alignments: List[DeltaAlignmen...
    method add_alignment (line 270) | def add_alignment(self, aln: DeltaAlignment) -> None:
    method __eq__ (line 277) | def __eq__(self, other):
    method __len__ (line 284) | def __len__(self):
    method __str__ (line 287) | def __str__(self):
  class DeltaIterator (line 292) | class DeltaIterator:
    method __init__ (line 303) | def __init__(self, handle: TextIO) -> None:
    method __iter__ (line 313) | def __iter__(self):
    method __next__ (line 317) | def __next__(self):

FILE: pyani/pyani_classify.py
  class Cliquesinfo (line 51) | class Cliquesinfo(NamedTuple):
  function build_graph_from_results (line 61) | def build_graph_from_results(
  function analyse_cliques (line 115) | def analyse_cliques(graph: nx.Graph) -> Cliquesinfo:
  function all_components_k_complete (line 124) | def all_components_k_complete(graph: nx.Graph) -> bool:
  function k_complete_component_status (line 132) | def k_complete_component_status(graph: nx.Graph) -> List[bool]:
  function remove_low_weight_edges (line 151) | def remove_low_weight_edges(

FILE: pyani/pyani_config.py
  function params_mpl (line 156) | def params_mpl(dfm: pd.DataFrame) -> Dict[str, Tuple[str, Any, Any]]:
  function get_colormap (line 183) | def get_colormap(dataframe: pd.DataFrame, matname: str) -> Tuple[str, An...

FILE: pyani/pyani_files.py
  class PyaniFilesException (line 53) | class PyaniFilesException(PyaniException):
  function get_fasta_files (line 59) | def get_fasta_files(dirname: Path = Path(".")) -> List[Path]:
  function get_fasta_paths (line 69) | def get_fasta_paths(
  function get_fasta_and_hash_paths (line 89) | def get_fasta_and_hash_paths(dirname: Path = Path(".")) -> List[Tuple[Pa...
  function get_input_files (line 118) | def get_input_files(dirname: Path, *ext) -> List[Path]:
  function get_sequence_lengths (line 128) | def get_sequence_lengths(fastafilenames: Iterable[Path]) -> Dict[str, int]:
  function read_hash_string (line 146) | def read_hash_string(filename: Path) -> Tuple[str, str]:
  function read_fasta_description (line 163) | def read_fasta_description(filename: Path) -> str:
  function load_classes_labels (line 175) | def load_classes_labels(path: Path) -> Dict[str, str]:
  function collect_existing_output (line 196) | def collect_existing_output(dirpath: Path, program: str, args: Namespace...

FILE: pyani/pyani_graphics/__init__.py
  class Params (line 64) | class Params:  # pylint: disable=too-few-public-methods
    method __init__ (line 68) | def __init__(
    method vdiff (line 87) | def vdiff(self):

FILE: pyani/pyani_graphics/mpl/__init__.py
  function clean_axis (line 72) | def clean_axis(axis):
  function add_dendrogram (line 84) | def add_dendrogram(dfr, fig, params, heatmap_gs, orientation="col"):
  function distribution (line 139) | def distribution(dfr, outfilename, matname, title=None):
  function get_heatmap_axes (line 179) | def get_heatmap_axes(dfr, fig, heatmap_gs):
  function add_colorbar (line 196) | def add_colorbar(dfr, fig, dend, params, orientation="row"):
  function add_labels (line 243) | def add_labels(heatmap_axes, rowlabels, collabels, params):
  function add_colorscale (line 265) | def add_colorscale(fig, heatmap_gs, ax_map, params, title=None):
  function heatmap (line 295) | def heatmap(dfr, outfilename=None, title=None, params=None):
  function scatter (line 363) | def scatter(

FILE: pyani/pyani_graphics/sns/__init__.py
  function get_colorbar (line 51) | def get_colorbar(dfr, classes):
  function add_labels (line 84) | def add_labels(fig, params):
  function get_clustermap (line 102) | def get_clustermap(dfr, params, title=None, annot=True):
  function heatmap (line 154) | def heatmap(dfr, outfilename=None, title=None, params=None):
  function distribution (line 192) | def distribution(dfr, outfilename, matname, title=None):
  function scatter (line 236) | def scatter(

FILE: pyani/pyani_jobs.py
  class Job (line 76) | class Job(object):
    method __init__ (line 80) | def __init__(self, name: str, command: str, queue: Optional[str] = Non...
    method add_dependency (line 96) | def add_dependency(self, job) -> None:
    method remove_dependency (line 105) | def remove_dependency(self, job) -> None:
    method wait (line 112) | def wait(self, interval: float = SGE_WAIT) -> None:
  class JobGroup (line 123) | class JobGroup(object):
    method __init__ (line 127) | def __init__(
    method generate_script (line 163) | def generate_script(self) -> None:
    method add_dependency (line 200) | def add_dependency(self, job) -> None:
    method remove_dependency (line 210) | def remove_dependency(self, job) -> None:
    method wait (line 217) | def wait(self, interval: float = SGE_WAIT) -> None:

FILE: pyani/pyani_orm.py
  class PyaniORMException (line 71) | class PyaniORMException(PyaniException):
  class LabelTuple (line 99) | class LabelTuple(NamedTuple):
  class Label (line 106) | class Label(Base):
    method __str__ (line 123) | def __str__(self) -> str:
    method __repr__ (line 131) | def __repr__(self) -> str:
  class BlastDB (line 138) | class BlastDB(Base):
    method __str__ (line 163) | def __str__(self) -> str:
    method __repr__ (line 171) | def __repr__(self) -> str:
  class Genome (line 178) | class Genome(Base):
    method __str__ (line 218) | def __str__(self) -> str:
    method __repr__ (line 222) | def __repr__(self) -> str:
  class Run (line 227) | class Run(Base):
    method __str__ (line 253) | def __str__(self) -> str:
    method __repr__ (line 257) | def __repr__(self) -> str:
  class Comparison (line 262) | class Comparison(Base):
    method __str__ (line 304) | def __str__(self) -> str:
    method __repr__ (line 320) | def __repr__(self) -> str:
  function create_db (line 325) | def create_db(dbpath: Path) -> None:
  function get_session (line 334) | def get_session(dbpath: Path) -> Any:
  function get_comparison_dict (line 344) | def get_comparison_dict(session: Any) -> Dict[Tuple, Any]:
  function get_matrix_labels_for_run (line 368) | def get_matrix_labels_for_run(session: Any, run_id: int) -> Dict:
  function get_matrix_classes_for_run (line 392) | def get_matrix_classes_for_run(session: Any, run_id: int) -> Dict[str, L...
  function filter_existing_comparisons (line 416) | def filter_existing_comparisons(
  function add_run (line 494) | def add_run(session, method, cmdline, date, status, name):
  function add_run_genomes (line 520) | def add_run_genomes(
  function update_comparison_matrices (line 618) | def update_comparison_matrices(session, run) -> None:

FILE: pyani/pyani_report.py
  function colour_rows (line 50) | def colour_rows(
  function table_padding (line 70) | def table_padding() -> Dict[str, Any]:
  function hover_highlight (line 75) | def hover_highlight(hover_colour: str = "#FFFF99") -> Dict[str, Any]:
  function header_font (line 83) | def header_font() -> Dict[str, Any]:
  function colour_identity (line 95) | def colour_identity(
  function colour_coverage (line 110) | def colour_coverage(
  function colour_numeric (line 125) | def colour_numeric(val: float, threshold: float = 0.95, colour: str = "#...
  function write_styled_html (line 138) | def write_styled_html(
  function write_to_stdout (line 176) | def write_to_stdout(
  function write_dbtable (line 191) | def write_dbtable(

FILE: pyani/pyani_tools.py
  class MatrixData (line 66) | class MatrixData(NamedTuple):
  class Dependencies (line 75) | class Dependencies(NamedTuple):
  class ANIResults (line 85) | class ANIResults:
    method __init__ (line 89) | def __init__(self, labels: List[str], mode: str) -> None:
    method add_tot_length (line 108) | def add_tot_length(
    method add_sim_errors (line 126) | def add_sim_errors(
    method add_pid (line 140) | def add_pid(
    method add_coverage (line 155) | def add_coverage(
    method hadamard (line 170) | def hadamard(self) -> float:
    method data (line 175) | def data(self) -> Iterator[Tuple[Any, str]]:
  class BLASTfunctions (line 199) | class BLASTfunctions(NamedTuple):
  class BLASTexes (line 207) | class BLASTexes(NamedTuple):
  class BLASTcmds (line 216) | class BLASTcmds:
    method __init__ (line 220) | def __init__(
    method build_db_cmd (line 235) | def build_db_cmd(self, fname: Path) -> str:
    method get_db_name (line 242) | def get_db_name(self, fname: Path) -> str:
    method build_blast_cmd (line 249) | def build_blast_cmd(self, fname: Path, dbname: Path):
  function get_labels (line 263) | def get_labels(filename: Path, logger: Optional[Logger] = None) -> Dict:
  function get_genome_length (line 293) | def get_genome_length(filename: Path) -> int:
  function label_results_matrix (line 303) | def label_results_matrix(matrix: pd.DataFrame, labels: Dict) -> pd.DataF...
  function has_dependencies (line 325) | def has_dependencies() -> Dependencies:
  function termcolor (line 333) | def termcolor(

FILE: pyani/run_multiprocessing.py
  function run_dependency_graph (line 56) | def run_dependency_graph(
  function populate_cmdsets (line 87) | def populate_cmdsets(job: Job, cmdsets: List, depth: int) -> List:
  function multiprocessing_run (line 113) | def multiprocessing_run(

FILE: pyani/run_sge.py
  function split_seq (line 57) | def split_seq(iterable: Iterable, size: int) -> Generator:
  function build_joblist (line 71) | def build_joblist(jobgraph) -> List:
  function compile_jobgroups_from_joblist (line 87) | def compile_jobgroups_from_joblist(
  function run_dependency_graph (line 116) | def run_dependency_graph(
  function populate_jobset (line 188) | def populate_jobset(job: Job, jobset: Set, depth: int) -> Set:
  function build_directories (line 206) | def build_directories(root_dir: Path) -> None:
  function build_job_scripts (line 233) | def build_job_scripts(root_dir: Path, jobs: List) -> None:
  function extract_submittable_jobs (line 248) | def extract_submittable_jobs(waiting: List) -> List:
  function submit_safe_jobs (line 264) | def submit_safe_jobs(
  function submit_jobs (line 314) | def submit_jobs(root_dir: Path, jobs: Iterable, sgeargs: Optional[str] =...
  function build_and_submit_jobs (line 333) | def build_and_submit_jobs(

FILE: pyani/scripts/__init__.py
  class PyaniScriptException (line 12) | class PyaniScriptException(Exception):
    method __init__ (line 16) | def __init__(self, msg="Error in pyani.py script"):
  function make_outdir (line 21) | def make_outdir(outdir: Path, force: bool, noclobber: bool) -> None:

FILE: pyani/scripts/average_nucleotide_identity.py
  function parse_cmdline (line 160) | def parse_cmdline(argv: Optional[List] = None) -> Namespace:
  function last_exception (line 437) | def last_exception() -> str:
  function make_outdirs (line 444) | def make_outdirs(args: Namespace):
  function compress_delete_outdir (line 477) | def compress_delete_outdir(outdir: Path, logger: Logger) -> None:
  function calculate_anim (line 489) | def calculate_anim(
  function calculate_tetra (line 582) | def calculate_tetra(infiles: List[Path]) -> pd.DataFrame:
  function make_sequence_fragments (line 615) | def make_sequence_fragments(
  function run_blast (line 639) | def run_blast(
  function unified_anib (line 694) | def unified_anib(
  function write (line 768) | def write(args: Namespace, results: pd.DataFrame) -> None:
  function draw (line 798) | def draw(args: Namespace, filestems: List[str], gformat: str) -> None:
  function subsample_input (line 831) | def subsample_input(args: Namespace, logger: Logger, infiles: List[Path]...
  function process_arguments (line 865) | def process_arguments(args: Optional[Namespace]) -> Namespace:
  function test_class_label_paths (line 884) | def test_class_label_paths(args: Namespace, logger: Logger) -> None:
  function get_method (line 900) | def get_method(args: Namespace) -> Tuple:
  function test_scheduler (line 928) | def test_scheduler(args: Namespace, logger: Logger) -> None:
  function run_main (line 947) | def run_main(argsin: Optional[Namespace] = None) -> int:

FILE: pyani/scripts/delta_filter_wrapper.py
  function run_main (line 70) | def run_main() -> int:

FILE: pyani/scripts/genbank_get_genomes_by_taxon.py
  class NCBIDownloadException (line 70) | class NCBIDownloadException(Exception):
    method __init__ (line 74) | def __init__(self):
  function parse_cmdline (line 80) | def parse_cmdline(argv=None):
  function last_exception (line 186) | def last_exception():
  function set_ncbi_email (line 193) | def set_ncbi_email(args: Namespace) -> None:
  function make_outdir (line 206) | def make_outdir(args: Namespace) -> None:
  function entrez_retry (line 251) | def entrez_retry(args, func, *fnargs, **fnkwargs):
  function entrez_batch_webhistory (line 284) | def entrez_batch_webhistory(args, record, expected, batchsize, *fnargs, ...
  function get_asm_uids (line 315) | def get_asm_uids(args, taxon_uid):
  function extract_filestem (line 352) | def extract_filestem(data):
  function get_ncbi_asm (line 370) | def get_ncbi_asm(args, asm_uid, fmt="fasta"):
  function retrieve_asm_contigs (line 453) | def retrieve_asm_contigs(
  function extract_archive (line 564) | def extract_archive(archivepath):
  function write_contigs (line 594) | def write_contigs(args, asm_uid, contig_uids, batchsize=10000):
  function logreport_downloaded (line 691) | def logreport_downloaded(accn, skiplist, accndict, uidaccndict):
  function run_main (line 710) | def run_main(args=None):

FILE: pyani/scripts/parsers/__init__.py
  function parse_cmdline (line 65) | def parse_cmdline(argv: Optional[List] = None) -> Namespace:

FILE: pyani/scripts/parsers/anib_parser.py
  function build (line 51) | def build(

FILE: pyani/scripts/parsers/aniblastall_parser.py
  function build (line 48) | def build(

FILE: pyani/scripts/parsers/anim_parser.py
  function build (line 53) | def build(

FILE: pyani/scripts/parsers/classify_parser.py
  function build (line 48) | def build(

FILE: pyani/scripts/parsers/common_parser.py
  function build (line 46) | def build() -> ArgumentParser:

FILE: pyani/scripts/parsers/createdb_parser.py
  function build (line 48) | def build(

FILE: pyani/scripts/parsers/download_parser.py
  function build (line 49) | def build(

FILE: pyani/scripts/parsers/fastani_parser.py
  function build (line 47) | def build(

FILE: pyani/scripts/parsers/index_parser.py
  function build (line 48) | def build(

FILE: pyani/scripts/parsers/listdeps_parser.py
  function build (line 45) | def build(

FILE: pyani/scripts/parsers/plot_parser.py
  function build (line 48) | def build(

FILE: pyani/scripts/parsers/report_parser.py
  function build (line 48) | def build(

FILE: pyani/scripts/parsers/run_common_parser.py
  function build (line 46) | def build() -> ArgumentParser:

FILE: pyani/scripts/parsers/scheduling_parser.py
  function build (line 44) | def build() -> ArgumentParser:

FILE: pyani/scripts/pyani_script.py
  function run_main (line 79) | def run_main(argv: Optional[List[str]] = None) -> int:
  function add_log_headers (line 151) | def add_log_headers():

FILE: pyani/scripts/subcommands/subcmd_anib.py
  function subcmd_anib (line 68) | def subcmd_anib(args: Namespace) -> None:
  function generate_joblist (line 258) | def generate_joblist(
  function fragment_fasta_file (line 277) | def fragment_fasta_file(inpath: Path, outdir: Path, fragsize: int) -> Tu...

FILE: pyani/scripts/subcommands/subcmd_aniblastall.py
  function subcmd_aniblastall (line 46) | def subcmd_aniblastall(args: Namespace):

FILE: pyani/scripts/subcommands/subcmd_anim.py
  class ComparisonJob (line 75) | class ComparisonJob(NamedTuple):
  class RunData (line 87) | class RunData(NamedTuple):
  class ComparisonResult (line 96) | class ComparisonResult(NamedTuple):
  class ProgData (line 110) | class ProgData(NamedTuple):
  class ProgParams (line 117) | class ProgParams(NamedTuple):
  function subcmd_anim (line 128) | def subcmd_anim(args: Namespace) -> None:
  function generate_joblist (line 308) | def generate_joblist(
  function run_anim_jobs (line 378) | def run_anim_jobs(joblist: List[ComparisonJob], args: Namespace) -> None:
  function update_comparison_results (line 418) | def update_comparison_results(

FILE: pyani/scripts/subcommands/subcmd_classify.py
  class SubgraphData (line 56) | class SubgraphData(NamedTuple):
  function subcmd_classify (line 65) | def subcmd_classify(args: Namespace) -> int:
  function trimmed_graph_sequence (line 122) | def trimmed_graph_sequence(

FILE: pyani/scripts/subcommands/subcmd_createdb.py
  function subcmd_createdb (line 49) | def subcmd_createdb(args: Namespace) -> int:

FILE: pyani/scripts/subcommands/subcmd_download.py
  class Skipped (line 54) | class Skipped(NamedTuple):
  function configure_entrez (line 65) | def configure_entrez(args: Namespace) -> Optional[str]:
  function dl_info_to_str (line 79) | def dl_info_to_str(esummary, uid_class) -> str:
  function download_data (line 99) | def download_data(
  function extract_genomes (line 180) | def extract_genomes(args: Namespace, dlstatus: download.DLStatus, esumma...
  function hash_genomes (line 211) | def hash_genomes(
  function download_genome (line 236) | def download_genome(args: Namespace, filestem: str, tid: str, uid: str, ...
  function get_tax_asm_dict (line 322) | def get_tax_asm_dict(args: Namespace) -> Dict[str, List]:
  function parse_api_key (line 342) | def parse_api_key(args: Namespace) -> Optional[str]:
  function subcmd_download (line 363) | def subcmd_download(args: Namespace) -> int:

FILE: pyani/scripts/subcommands/subcmd_fastani.py
  class ComparisonJob (line 77) | class ComparisonJob(NamedTuple):
  class RunData (line 91) | class RunData(NamedTuple):
  class ComparisonResult (line 100) | class ComparisonResult(NamedTuple):
  function subcmd_fastani (line 114) | def subcmd_fastani(args: Namespace) -> None:
  function generate_joblist (line 298) | def generate_joblist(
  function run_fastani_jobs (line 371) | def run_fastani_jobs(joblist: List[ComparisonJob], args: Namespace) -> N...
  function update_comparison_results (line 416) | def update_comparison_results(

FILE: pyani/scripts/subcommands/subcmd_index.py
  function subcmd_index (line 53) | def subcmd_index(args: Namespace) -> int:

FILE: pyani/scripts/subcommands/subcmd_listdeps.py
  function subcmd_listdeps (line 54) | def subcmd_listdeps(args: Namespace) -> int:

FILE: pyani/scripts/subcommands/subcmd_plot.py
  function subcmd_plot (line 67) | def subcmd_plot(args: Namespace) -> int:
  function write_run_plots (line 102) | def write_run_plots(run_id: int, session, outfmts: List[str], args: Name...
  function write_distribution (line 180) | def write_distribution(
  function write_heatmap (line 206) | def write_heatmap(
  function write_scatter (line 243) | def write_scatter(

FILE: pyani/scripts/subcommands/subcmd_report.py
  class ReportParams (line 67) | class ReportParams(NamedTuple):
  function subcmd_report (line 75) | def subcmd_report(args: Namespace) -> int:
  function report (line 323) | def report(args: Namespace, session, formats: List[str], params: ReportP...
  function process_formats (line 382) | def process_formats(args: Namespace) -> List[str]:

FILE: pyani/tetra.py
  function calculate_tetra_zscores (line 66) | def calculate_tetra_zscores(infilenames: Iterable) -> Dict[str, Dict[str...
  function calculate_tetra_zscore (line 78) | def calculate_tetra_zscore(filename: Path) -> Dict[str, float]:
  function tetra_clean (line 143) | def tetra_clean(instr: str) -> bool:
  function calculate_correlations (line 158) | def calculate_correlations(tetra_z: Dict[str, Dict[str, float]]) -> pd.D...

FILE: tests/conftest.py
  class MockGenome (line 70) | class MockGenome(NamedTuple):
  class MockProcess (line 76) | class MockProcess(NamedTuple):
  class MockMatch (line 83) | class MockMatch(NamedTuple):
    method group (line 86) | def group(self):
  function blastall_available (line 91) | def blastall_available():
  function blastn_available (line 109) | def blastn_available():
  function dir_anib_in (line 122) | def dir_anib_in():
  function dir_anim_in (line 128) | def dir_anim_in():
  function dir_fastani_in (line 134) | def dir_fastani_in():
  function dir_graphics_in (line 140) | def dir_graphics_in():
  function dir_seq (line 146) | def dir_seq():
  function dir_targets (line 152) | def dir_targets():
  function dir_tgt_fragments (line 158) | def dir_tgt_fragments(dir_targets):
  function email_address (line 164) | def email_address():
  function executable_incompatible_with_os (line 170) | def executable_incompatible_with_os(monkeypatch):
  function executable_missing (line 201) | def executable_missing(monkeypatch):
  function executable_not_executable (line 218) | def executable_not_executable(monkeypatch):
  function executable_without_version (line 243) | def executable_without_version(monkeypatch):
  function fragment_length (line 278) | def fragment_length():
  function mock_get_nucmer_3_version (line 284) | def mock_get_nucmer_3_version(monkeypatch):
  function mock_get_nucmer_4_version (line 319) | def mock_get_nucmer_4_version(monkeypatch):
  function unsorted_genomes (line 351) | def unsorted_genomes(dir_anim_in):
  function mock_legacy_single_genome_dl (line 358) | def mock_legacy_single_genome_dl(monkeypatch):
  function mock_single_genome_dl (line 387) | def mock_single_genome_dl(monkeypatch):
  function mock_blochmannia_dl (line 429) | def mock_blochmannia_dl(monkeypatch):
  function mock_blochmannia_kraken_dl (line 660) | def mock_blochmannia_kraken_dl(monkeypatch):
  function nucmer_available (line 892) | def nucmer_available():
  function path_file_two (line 905) | def path_file_two():
  function path_file_four (line 911) | def path_file_four():
  function path_fixtures_base (line 917) | def path_fixtures_base():
  function path_fna (line 923) | def path_fna(dir_seq):
  function path_fna_two (line 930) | def path_fna_two(dir_seq):
  function path_fna_all (line 937) | def path_fna_all(dir_seq):
  function skip_by_unavailable_executable (line 943) | def skip_by_unavailable_executable(