pyani.pyani_tools module

Code to support pyani.

class pyani.pyani_tools.ANIResults(labels: List[str], mode: str)

Bases: object

Holds ANI dataframe results.

add_coverage(qname: str, sname: str, qcover: float, scover: Optional[float] = None) → None

Add percentage coverage values to self.alignment_coverage.

Parameters:

• qname –
• sname –
• value –
• sym –

add_pid(qname: str, sname: str, value: float, sym: bool = True) → None

Add a percentage identity value to self.percentage_identity.

Parameters:

• qname –
• sname –
• value –
• sym –

add_sim_errors(qname: str, sname: str, value: float, sym: bool = True) → None

Add a similarity error value to self.similarity_errors.

Parameters:

• qname –
• sname –
• value –
• sym –

add_tot_length(qname: str, sname: str, value: float, sym: bool = True) → None

Add a total length value to self.alignment_lengths.

Parameters:

• qname –
• sname –
• value –
• sym –

data

Return list of (dataframe, filestem) tuples.

hadamard

Return Hadamard matrix (identity * coverage).

class pyani.pyani_tools.BLASTcmds(funcs: pyani.pyani_tools.BLASTfunctions, exes: pyani.pyani_tools.BLASTexes, prefix: str, outdir: pathlib.Path)

Bases: object

Class for construction of BLASTN and database formatting commands.

build_blast_cmd(fname: pathlib.Path, dbname: pathlib.Path)

Return BLASTN command.

Parameters:

• fname – Path to query file
• dbname – Path to database

build_db_cmd(fname: pathlib.Path) → str

Return database format/build command.

Parameters:fname –

get_db_name(fname: pathlib.Path) → str

Return database filename.

Parameters:fname –

class pyani.pyani_tools.BLASTexes

Bases: tuple

Convenience structure to hold BLAST executables.

blast_exe

Alias for field number 1

format_exe

Alias for field number 0

class pyani.pyani_tools.BLASTfunctions

Bases: tuple

Convenience structure to hold BLAST functions.

blastn_func

Alias for field number 1

db_func

Alias for field number 0

class pyani.pyani_tools.Dependencies

Bases: tuple

Convenience struct for third-party dependency presence.

blast

Alias for field number 0

legacy_blast

Alias for field number 1

mummer

Alias for field number 2

class pyani.pyani_tools.MatrixData

Bases: tuple

Convenience struct for matrix data returned by ORM.

data

Alias for field number 1

graphic_args

Alias for field number 2

name

Alias for field number 0

pyani.pyani_tools.get_genome_length(filename: pathlib.Path) → int

Return total length of all sequences in a FASTA file.

Parameters:filename – path to FASTA file

pyani.pyani_tools.get_labels(filename: pathlib.Path, logger: Optional[logging.Logger] = None) → Dict[KT, VT]

Return dictionary of alternative sequence labels, or None.

Parameters:

• filename – path to file containing tab-separated table of labels
• logger – logging object

Input files should be formatted as <hash>t<key>t<label>, one pair per line.

pyani.pyani_tools.has_dependencies() → pyani.pyani_tools.Dependencies

Return NamedTuple indicating if 3rd dependencies are available.

pyani.pyani_tools.label_results_matrix(matrix: pandas.core.frame.DataFrame, labels: Dict[KT, VT]) → pandas.core.frame.DataFrame

Return results matrix dataframe with labels.

Parameters:

• matrix – results dataframe deriving from Run object
• labels – dictionary of genome labels labels must be keyed by index/col values from matrix

Applies the labels from the dictionary to the dataframe in matrix, and returns the result.

pyani.pyani_tools.termcolor(logstr: str, color: Optional[str] = None, bold: Optional[bool] = False) → str

Return the passed logstr, wrapped in terminal colouring.