ucscCancer/paradigm-scripts

Name: paradigm-scripts

Owner: UCSC Cancer Research

Description: null

Created: 2012-10-08 01:11:58.0

Updated: 2017-12-12 06:33:59.0

Pushed: 2015-02-17 01:13:05.0

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Size: 17768

Language: Python

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README

PARADIGM: Pathway Recognition Algorithm using Data Integration on Genomic Models

Current Version

1.0

Authors

Charles Vaske, Stephen Benz, Sam Ng, Kyle Ellrott, David Haussler and Joshua M. Stuart

Requirements

• python >= 2.7
• scipy >= 0.12.0
• numpy
• pandas

Installation

Note: This repository contains code that allows users to parallelize PARADIGM on a large cohort of samples, the PARADIGM binary is separate and may need to be compiled from https://sbenz.github.com/Paradigm

• Install dependencies
• Download the paradigm-scripts repository to the desired location
• Run “make” in paradigm-scripts/ to generate source files
• Source init files for paradigm-scripts (init.sh for bash and init.csh for csh)
• Run code on example data in examples/ with “make”

Command-Line

xyParadigm.py [options] attachment file:path [attachment file:path ...]

chment - dogma node to attach evidence to
:path - type of and path to evidence file

ork_directory - path to directory where work is to be done (default: ./)
ull_size - number of null samples to be generated per sample
ogma_library - path or zip file describing the PARADIGM plate model
athway_library - path, zip, or file containing PARADIGM pathway interactions
iscretization_bounds - value cutoffs for data discretization
aram_file - parameter file to use as initial state
 skip EM parameter training
 utilizing the public PARADIGM binary

Folders

• bin : executables
• dogmas : dogma plate models for PARADIGM
• examples : OV inputs for demonstration purposes
• exe : pre-compiled paradigm binaries for select architectures
• pathways : paradigm compatible pathway files