HiCtool_utility_code.md

HiCtool utility code

We provide a series of utility functions included into HiCtool_utilities.py that allow to work with HiCtool generated data in the Python environment, such as:

• Loading and saving HiCtool contact matrices (either in compressed and tab-separated format).
• Loading DI values or HMM states.
• Loading topological domain coordinates.

These functions will allow you to use HiCtool data for additional analyses, and eventually re-save to file your processed data in order to be plotted using HiCtool. You could even have contact matrices generated with other software, parse them into a numpy matrix format, and then save them using the saving functions in order to be normalized or plotted for example.

First, open your Python or iPython shell and execute the script:

execfile('HiCtool_utilities.py')

Then, call the function you need (see how to use each function in the function documentation inside the script):

• save_matrix to save a square and symmetric contact matrix (intra-chromosomal or global matrix) in the HiCtool compressed format.
• load_matrix to load a square and symmetric contact matrix (intra-chromosomal or global matrix) in the HiCtool compressed format.
• save_matrix_rectangular to save a rectangular contact matrix (inter-chromosomal) in the HiCtool compressed format.
• load_matrix_rectangular to load a rectangular contact matrix (inter-chromosomal) in the HiCtool compressed format.
• save_matrix_tab to save any contact matrix in the tab-separated format.
• load_matrix_tab to load any contact matrix in the tab-separated format.
• load_DI_values to load DI values.
• load_HMM_states to load HMM states.
• save_topological_domains to save topological domains values in tab-separated format.
• load_topological_domains to load topological domains values in tab-separated format.