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 on filed (value) which is a single integer being an output parameter of ReadNextKmer and CheckKmer methods of CKMCFile 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: Methods:

CKMCFile class

Fields: Methods: