mg-process-chas for ChAs

Table Of Content

• Requirements
• Installation
• Usage

Requirements

• pip and virtualenv
• Python 2.7.X
• Python Modules:
  • pylint
  • pytest
  • mg-tool-api

Installation

Create the Python environment

virtualenv -p /usr/bin/python2 .py2Env
source .py2Env/bin/activate
pip install --upgrade pip
pip install -r requirements.txt

Usage

1. Update all VM file paths in mug_generated_metadata to local paths

test_0_ComputeChromatineassortativityfromPChiCdata.sh:14:TOOL_EXECUTABLE=/home/pmes/mg-process-chas/process_chas.py
test_1_ComputeChromatineassortativityfromChicagodata.sh:14:TOOL_EXECUTABLE=/home/pmes/mg-process-chas/process_chas.py
json/0_ComputeChromatineassortativityfromPChiCdata/in_metadata.json:4:        "file_path": "/home/pmes/mg-process-chas/testing_data/PCHiC_interaction_map.txt",
json/0_ComputeChromatineassortativityfromPChiCdata/in_metadata.json:33:        "file_path": "/home/pmes/mg-process-chas/testing_data/Features_mESC.txt",
json/1_ComputeChromatineassortativityfromChicagodata/in_metadata.json:4:        "file_path": "/home/pmes/mg-process-chas/testing_data/PCHiC_interaction_map_BAD.txt",
json/1_ComputeChromatineassortativityfromChicagodata/

2. Run ./mug_generated_metadata/test_0_ComputeChromatineassortativityfromPChiCdata.sh