FastANI

FastANI (Jain, C., Rodriguez-R, L.M., Phillippy, A.M. et al.)

Basic usage

from chiton.fastani import fastani

result = fastani(query='query.fna', reference='reference.fna')
dict_results = result.as_dict()

# Accessing results
print(dict_results['query.fna']['reference.fna'].ani)         # 89.1234
print(dict_results['query.fna']['reference.fna'].n_frag)      # 50
print(dict_results['query.fna']['reference.fna'].total_frag)  # 100
print(dict_results['query.fna']['reference.fna'].align_frac)  # 0.5

# Writing results to disk
result.to_file('results.txt')

Models

Input

chiton.fastani.fastani(query, reference, k=None, cpus=None, frag_len=None, min_frac=None, min_frag=None, single_execution=True, bidirectional=False, exe='fastANI', tmp_root='/tmp', show_progress=True)

Run FastANI on a set of paths.

Parameters

query (Union[str, Collection[str]]) – Either a path to the query genome, or a collection of paths to query genomes.
reference (Union[str, Collection[str]]) – Either a path to the reference genome, or a collection of paths to reference genomes.
k (Optional[int]) – kmer size <= 16 (default: 16).
cpus (Optional[int]) – Number of CPUs to use (default: 1).
frag_len (Optional[int]) – fragment length (default: 3,000).
min_frac (Optional[float]) – minimum fraction of genome that must be shared for trusting ANI (default: 0.2) [version >= 1.3].
min_frag (Optional[int]) – minimum matched fragments for trusting ANI (default: 50) [version <= 1.2].
single_execution (bool) – True if –refList and –queryList should be used, otherwise a subprocess will be launched to do 1:1 comparisons.
bidirectional (bool) – True if the ANI should be calculated for query vs reference and vice-versa.
exe (str) – The path to the execution file.
tmp_root (str) – The root directory used to write temporary files to.
show_progress (bool) – True if a progress bar should be shown, False otherwise.

Return type

FastANIResults

Output

class chiton.fastani.model.FastANIResults(query, reference, executions, params)

The results from a FastANI method request.

as_dict()

Returns the results as a dictionary of query -> reference values.

Examples

>>> result = fastani(query='query.fna', reference='reference.fna')
>>> d_results = results.as_dict()
>>> d_results['query.fna']['reference.fna'].align_frac)
0.8

Return type: Dict[str, Dict[str, Optional[FastANIResult]]]

executions: The outcome of each FastANIExecution.

iter_results()

Returns an iterator of the query, reference, and results. NOTE: This will only return those which had >=80% ANI.

Return type: Iterator[Tuple[str, str, Optional[FastANIResult]]]

params: The FastANIParameters used in the execution.

query: A collection of paths to the query genomes.

reference: A collection of paths to the reference genomes.

class chiton.fastani.model.FastANIResult(ani, n_frag, total_frag)

The data associated with a FastANI output file.

align_frac: The alignment fraction

ani: The percentage of ANI

n_frag: The number of aligned fragments

total_frag: The total number of fragments

Helper classes

class chiton.fastani.model.FastANIExecution(cmd, stdout, stderr, return_code, output)

The input, output and logs of a single FastANI execution.

cmd: The command used to execute FastANI

output: The output of the execution, None if ANI <80%

return_code: The return code of the execution

stderr: The stderr of the execution

stdout: The stdout of the execution

class chiton.fastani.model.ResultFile(path)

A wrapper to the FastANI output file.

data: A map of (query path, reference path) = result

class chiton.fastani.model.FastANIParameters(version, exe, single_execution=True, bidirectional=False, k=None, cpus=None, frag_len=None, min_frac=None, min_frag=None)

An interface to the parameters selected for execution.

bidirectional: True if the ANI should be calculated for query vs reference and vice-versa.

cpus: The number of CPUs to use.

exe: The path to the FastANI executable.

frag_len: The minimum fragment length.

k: The k-mer size.

min_frac: Minimum fraction of genome that must be shared for trusting ANI [version >= 1.3].

min_frag: Minimum matched fragments for trusting ANI [version <= 1.2].

single_execution: True if –refList and –queryList should be used, otherwise a subprocess will be launched to do 1 to 1 comparisons.

version: The version of FastANI.