Python wrapper for KMC API

Python wrapper for C++ KMC API is made to mimic C++ API interface. C++ are python are very different languages, so some compromise needs to be made. For example in python it is not possible to pass integer by reference, but in C++ KMC API this is the way the counter of k-mer is returnet. One (rather ugly) workaroud is to wrap integer in a class that is passed by reference in python.

py_kmc_api module contains following classes:

• CountVec - it contains one filed (value) which is a list of integers being an output parameter of GetCountersForRead method of CKMCFile class.
• Count - it contains one filed (value) which is a single integer being an output parameter of ReadNextKmer and CheckKmer methods of CKMCFile class.
• LongKmerRepresentation - it contains one field (value) wich is a list of integers being a binary k-mer representation (each integer is, at C++ side 8 byte unsigned), it is used in to_long method of KmerAPI class
• CKMCFileInfo - contains base information of KMC database.
• CKmerAPI - represents a single k-mer.
• CKMCFile - represents a KMC database, that may be opened in one of two modes: listing(only part of it is loaded into memory, privides sequential access to the database), random access (whole database is loaded into memory, provides existence query of a specific k-mer).

The public interface of this classes is described below.

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CKMCFileInfo class

Fields:

• kmer_length - the length of a k-mer
• mode - always 0 (1 for older versions of KMC where quake aware counters were supported)
• counter_size - the numer of bytes used to store each counter in kmc database
• lut_prefix_length - internal parameter of kmc database, see more details in API.pdf
• signature_len - the length of signature (it is also internal parameter used while database was constructed)
• min_count - minimum value of a counter (if some k-mer had lower occurences than this value it is not stored in the database)
• max_count - maximal value of a counter (if some k-mer had higher occurences than this value it is not store int the database)
• both_strands - True if kmc was run with -b switch, False otherwise
• total_kmers - the total numer of k-mers stored in the database

Methods: None

CKmerAPI class

Fields: None Methods:

• init(length) - constructor, takes one parameter, the length of a k-mer (may be skipped then 1 is taken as a default value)
• init(kmer: KmerAPI) - constructor that created new object beased on existing one (copy ctor in C++ nomenclature)
• assign(kmer: KmerAPI) - replace kmer with the one passed by parameter (equivalent of C++ copy assignment operator)
• eq(kmer: KmerAPI) - equality comparison
• lt(kmer: KmerAPI) - lower than comparison
• get_asci_symbol(pos) - returns symbol at 0-based position
• get_num_symbol(pos) - same as get_asci_sybol, but encoded (A->0, C->1, G->2, T->3)
• str - converts k-mer to string representation
• to_long(result: LongKmerRepresentation ) - converts k-mer to list of integers being its binary representation (each integer is unsigned 8 byte integer at C++ side)
• reverse - converts k-mer to its reverse complement
• get_signature(sig_len) - get the numeric representation of signature of a k-mer. Signature is internal term and generalization of minimizer used to achieve better performance of KMC, the concept is described in detains in the paper describing KMC 2
• from_string(kmer_str) - converts string k-mer representation to internal KmerAPI representation

CKMCFile class

Fields: Methods: