Kssd API

The Kssd class provides functionalities for processing and analyzing k-mer based sketches, with methods for updating, storing, comparing, and managing sketches.

C++ Interface

kssd_parameter_t(int half_k_, int half_subk_, int drlevel_, string shuffle_file)

Constructs a kssd_parameter_t object with the specified parameters.

Parameters:

half_k_ (int): Half of the k-mer size used for hashing.
half_subk_ (int): Half of the sub k-mer size for dimensionality reduction.
drlevel_ (int): Dimensionality reduction level.
shuffle_file (string): Path to the file containing the shuffled dimension map.

Kssd(kssd_parameter_t params)

Constructs a Kssd object with the specified parameters.

Parameters:

params (kssd_parameter_t): A parameter object containing configuration for Kssd.

void update(const char *seq)

Updates the Kssd object with the provided sequence.

Parameters:

seq (const char*): A pointer to the sequence to be processed.

vector<uint32_t> storeHashes()

Retrieves the stored 32-bit hashes from the Kssd object.

Returns:

vector<uint32_t>: A vector of 32-bit hashes.

vector<uint64_t> storeHashes64()

Retrieves the stored 64-bit hashes from the Kssd object.

Returns:

vector<uint64_t>: A vector of 64-bit hashes.

void loadHashes(std::vector<uint32_t> hashArr)

Loads a list of 32-bit hashes into the Kssd object.

Parameters:

hashArr (std::vector<uint32_t>): A vector of 32-bit hashes to load.

void loadHashes64(std::vector<uint64_t> hashArr)

Loads a list of 64-bit hashes into the Kssd object.

Parameters:

hashArr (std::vector<uint64_t>): A vector of 64-bit hashes to load.

double jaccard(Kssd *kssd)

Computes the Jaccard similarity between this Kssd object and another.

Parameters:

kssd (Kssd**): A pointer to another Kssd object to compare against.

Returns:

double: The Jaccard similarity value.

double distance(Kssd *kssd)

Computes the Mash distance between this Kssd object and another.

Parameters:

kssd (Kssd**): A pointer to another Kssd object to compare against.

Returns:

double: The Mash distance value.

void transSketches(vector<KssdLite> &sketches, sketchInfo_t &info, string dictFile, string indexFile, int numThreads)

Transforms KssdLite sketches for indexing purposes.

Parameters:

sketches (vector<KssdLite>&): A reference to the vector of KssdLite sketches.
info (sketchInfo_t&): Metadata associated with the sketches.
dictFile (string): Path to the dictionary file.
indexFile (string): Path to the index file.
numThreads (int): The number of threads to use.

void index_tridist(vector<KssdLite> &sketches, sketchInfo_t &info, string refSketchOut, string outputFile, int kmer_size, double maxDist, int isContainment, int numThreads)

Computes the sketch index using a distance-based method.

Parameters:

sketches (vector<KssdLite>&): A reference to the vector of KssdLite sketches.
info (sketchInfo_t&): Metadata associated with the sketches.
refSketchOut (string): Path to save the reference sketches.
outputFile (string): Path to the output file.
kmer_size (int): Size of the k-mers.
maxDist (double): Maximum allowed distance.
isContainment (int): Whether to use containment comparison.
numThreads (int): The number of threads to use.

void saveSketches(vector<KssdLite> &sketches, sketchInfo_t &info, string outputFile)

Saves the KssdLite sketches to a specified file.

Parameters:

sketches (vector<KssdLite>&): A reference to the vector of KssdLite sketches.
info (sketchInfo_t&): Metadata associated with the sketches.
outputFile (string): Path to the output file.

bool isSketchFile(string inputFile)

Checks if the given file has a .sketch extension.

Parameters:

inputFile (string): The file name to check.

Returns:

bool: true if the file is a .sketch file, otherwise false.

void printInfos(vector<Sketch::Kssd*> &sketches, string outputFile)

Prints basic information about the sketches to the specified file.

Parameters:

sketches (vector<Sketch::Kssd>&*): A reference to the vector of Sketch::Kssd objects.
outputFile (string): Path to the output file.

void printSketches(vector<Sketch::Kssd*> &sketches, string outputFile)

Prints detailed information about the sketches, including all stored hashes.

Parameters:

sketches (vector<Sketch::Kssd>&*): A reference to the vector of Sketch::Kssd objects.
outputFile (string): Path to the output file.

KssdLite toLite() const

Converts the current Kssd object into a lightweight KssdLite representation.

Returns:

KssdLite: A lightweight representation of the Kssd object.

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Python Interface

Kssd(kssd_parameter_t params)

Constructs a Kssd object with the specified parameters.

Parameters:

params (kssd_parameter_t): A parameter object containing configuration for Kssd.

class Kssd(params: kssd_parameter_t)

Constructs a Kssd object in Python.

Parameters:

params (kssd_parameter_t): Configuration parameters for the Kssd object.

void update(const char *seq)

Updates the Kssd object with the provided sequence.

Parameters:

seq (const char*): A pointer to the sequence to be processed.

update(seq: str)

Updates the sketch with the given sequence.

Parameters:

seq (str): The sequence to be processed.

double jaccard(Kssd *kssd)

Computes the Jaccard similarity between this Kssd object and another.

Parameters:

kssd (Kssd**): A pointer to another Kssd object to compare against.

Returns:

double: The Jaccard similarity value.

jaccard(other: Kssd) → float

Computes the Jaccard similarity between this sketch and another.

Parameters:

other (Kssd): The other Kssd object to compare.

Returns:

float: The Jaccard similarity value.

double distance(Kssd *kssd)

Computes the Mash distance between this Kssd object and another.

Parameters:

kssd (Kssd**): A pointer to another Kssd object to compare against.

Returns:

double: The Mash distance value.

distance(other: Kssd) → float

Computes the Mash distance between this sketch and another.

Parameters:

other (Kssd): The other Kssd object to compare.

Returns:

float: The Mash distance value.

vector<uint32_t> storeHashes()

Retrieves the stored 32-bit hashes from the Kssd object.

Returns:

vector<uint32_t>: A vector of 32-bit hashes.

store_hashes() → list[int]

Retrieves the stored 32-bit hashes.

Returns:

list[int]: A list of 32-bit hashes.

KssdLite toLite() const

Converts the current Kssd object into a lightweight KssdLite representation.

Returns:

KssdLite: A lightweight representation of the Kssd object.

toLite() → KssdLite

Converts the current Kssd object to a lightweight KssdLite representation.

Returns:

KssdLite: A lightweight representation of the Kssd object.

kssd_parameter_t(int half_k_, int half_subk_, int drlevel_, string shuffle_file)

Constructs a kssd_parameter_t object with the specified parameters.

Parameters:

half_k_ (int): Half of the k-mer size used for hashing.
half_subk_ (int): Half of the sub k-mer size for dimensionality reduction.
drlevel_ (int): Dimensionality reduction level.
shuffle_file (string): Path to the shuffle file containing dimension map.

class kssd_parameter_t(half_k: int, half_subk: int, drlevel: int, shuffle_file: str)

Represents the parameter set used for configuring the Kssd object.

Parameters:

half_k (int): Half of the k-mer size used for hashing.
half_subk (int): Half of the sub k-mer size for dimensionality reduction.
drlevel (int): Dimensionality reduction level.
shuffle_file (str): Path to the shuffle file containing dimension map.

save_sketches(sketches: list[KssdLite], info: SketchInfo, filename: str)

Saves a list of KssdLite sketches to a specified file.

Parameters:

sketches (list[KssdLite]): A list of sketches to save.
info (SketchInfo): Metadata associated with the sketches.
filename (str): Path to the file where the sketches will be saved.

trans_sketches(sketches: list[KssdLite], info: SketchInfo, dict_file: str, index_file: str, num_threads: int)

Transforms KssdLite sketches into a format suitable for indexing.

Parameters:

sketches (list[KssdLite]): A list of sketches to transform.
info (SketchInfo): Metadata associated with the sketches.
dict_file (str): Path to the dictionary file used for transformation.
index_file (str): Path to the index file used for transformation.
num_threads (int): Number of threads for parallel processing.

index_dict(sketches: list[KssdLite], info: SketchInfo, ref_sketch_out: str, output_file: str, kmer_size: int, max_dist: float, is_containment: bool, num_threads: int)

Computes the sketch index using a distance-based dictionary approach.

Parameters:

sketches (list[KssdLite]): A list of sketches to process.
info (SketchInfo): Metadata associated with the sketches.
ref_sketch_out (str): Path to save the reference sketches.
output_file (str): Path to the file where results will be saved.
kmer_size (int): Size of the k-mers used for sketching.
max_dist (float): Maximum allowed distance for comparisons.
is_containment (bool): Whether to use containment comparisons.
num_threads (int): Number of threads for parallel processing.