Examples of how to run khmer command-line scripts are included in the main khmer documentation, as well as the khmer protocols collection. This document is intended for programmers and developers who want to use khmer's Python or C++ API.
Note: The khmer command-line scripts are under semantic versioning, but (as of khmer v2) neither the Python API nor the C++ API are covered under semantic versioning. Consequently, updates to the khmer code base may require changes to the examples below at any time. We expect to have the Python API under semantic versioning by version 5.0.
The following example demonstrates the basics of counting k-mers with khmer.
>>> import khmer
>>>
>>> ksize = 11
>>>
>>> # exact counting with and odd k requires a single table with 4^k bytes
>>> # even k will collapse k-mers with their reverse complement, and requires 4^(k-1) + k bytes
>>> cg = khmer.Countgraph(ksize, 4**ksize, 1)
>>>
>>> # load all k-mers from the given string (returns the number of k-mers processed)
>>> cg.consume('ATGGCGATGGCAAGTAGGACCCAGATGGACCAAAG')
25
>>>
>>> # what is the count of the k-mer "ATGGCGATGGC"?
>>> cg.get('ATGGCGATGGC')
1
>>> # increase the count of the k-mer by 1
>>> cg.add('ATGGCGATGGC')
1
>>> # what is the k-mer's count now?
>>> cg.get('ATGGCGATGGC')
2
>>>
>>> # what is the count of this bogus k-mer?
>>> cg.get('GTGGCGATGGC')
0
>>>
The count-stuff.cpp file in the examples/c++-api/ directory contains source code that calls khmer's C++ API directly. To run this example, issue the following commands from your terminal. The Makefile in examples/c++-api/ shows how to compile and link against the khmer library.
cd examples/c++-api/
make
./count-stuff