Straw is library which allows rapid streaming of contact data from .hic files. This repository contains source code for the C++, R, Python, and MATLAB versions of Straw.
For the Java version of Straw, see: https://github.com/aidenlab/java-straw/
For the Javascript version of Straw, see: https://github.com/igvteam/hic-straw/
There are two Python versions - a pure Python one and a version where the C++ code is bound with pybind11. The former version is deprecated in favor of using the pybind11 version, which is much faster.
A Jupyter notebook example can be found here: https://aidenlab.gitbook.io/juicebox/accessing-raw-data
For the fastest version, you must have pybind11 installed.
Clone the library and cd into the straw/ directory.
pip install ./pybind11_python
Then run via import strawC and strawC.strawC
Example:
>>>import strawC
>>>result = strawC.strawC('NONE', 'HIC001.hic', 'X', 'X', 'BP', 1000000)
>>>for i in range(len(result)):
... print("{0}\t{1}\t{2}".format(result[i].binX, result[i].binY, result[i].counts))
g++ -std=c++0x -o straw main.cpp straw.cpp -lcurl -lz
Please see the wiki for more documentation.
For questions, please use the Google Group.
Ongoing development work is carried out by Muhammad S. Shamim, Craig Wenger, and Neva C. Durand.
If you use this tool in your work, please cite
Neva C. Durand, James T. Robinson, Muhammad S. Shamim, Ido Machol, Jill P. Mesirov, Eric S. Lander, and Erez Lieberman Aiden. "Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom." Cell Systems 3(1), 2016.