straw's Introduction

straw: Extract data quickly from Juicebox via straw

Straw is a fast implementation of reading/dump for .hic files. Available in C++, R, and Python.

There are two Python versions - a pure Python one and a version where the C++ code is bound with pybind11. The latter is much faster.

Quick Start Python

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))

For the pure Python version:

pip install ./python

Then run via import straw and straw.straw

Some more information on running: https://github.com/aidenlab/straw/tree/master/python

Compile on Linux

     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 Neva C. Durand and Yue Wu.

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.

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