diff --git a/README.md b/README.md index 1a7044e97bc5cbab2340d78e9d5997012a5bdddf..d2d9dba06b498eea11b7438d8d39b658fa0166e6 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,26 @@ # kmatch -- on the scicore ubuntu system, you do `source ubuntu_compile` to execute the compile command therein -- on other systems: good luck -- usage examples are in the two Python scripts. Make sure to read the comments therein before executing -- before you can execute the scripts with Python, you need to load the exact same Python module as for compiling +Simple k-mer counting for ultrafast screening of large sequence databases in Python. You're at the wrong place if you look for highly sensitive sequence searches. Usage examples: + +* create_db.py - Builds search index for user defined k-mer size k. +* search_db.py - Search previously built index. The index is optionally loaded in memory to speed up repeated searches on the same index. + +Setup +----- +Dependencies: +* A recent c++ compiler supporting C++11 +* Python 3 +* pybind11 (https://github.com/pybind/pybind11) + +Compile: +``` +g++ -O3 -Wall -shared -std=c++11 -fPIC $(python3-config --includes) -I<path_to_pybind11>/include kmat +ch.cpp -o kmatch$(python3-config --extension-suffix) +``` + +Tell Python where to find the library: +``` +export PYTHONPATH=<path_to_compile_dir>:$PYTHONPATH +``` + +Test it with the provided example scripts! \ No newline at end of file