Source code for direct_interactions_test
#!/usr/bin/python
'''
Direct interactions test
============================
'''
[docs]def run():
'''
This is a simple Python script for generating permuted mutation data. The
default parameter values are for permuting the GBM(2008) mutation data in
the examples/mutation_data/GBM_2008 directory, which is a small dataset.
The main utility of this script is that it is much faster to generate
permutation data before running the permutation test.
Note: on my machine, it takes ~3 seconds to permute the mutation data
*once*.
'''
# Load required modules
import sys, os
sys.path.insert(1, os.path.abspath('../../lib'))
import permute_mutation_data as P
# Default parameters for this tutorial (CHANGE AT YOUR OWN RISK)
MUTATION_MATRIX="../mutation_data/GBM_2008/GBM_2008.m2"
CUTOFF=2
NUM_MATRICES=1
OUTPUT_DIR="./sample_output/permuted_matrices"
GENE_BLACKLIST="../mutation_data/fishy_genes.glst"
GENE_WHITELIST=None
PATIENT_WHITELIST=None
PATIENT_BLACKLIST=None
args = [ "-m", MUTATION_MATRIX, "-c", CUTOFF, "-o", OUTPUT_DIR, "-v" ]
if GENE_BLACKLIST: args += [ "-bg", GENE_BLACKLIST ]
if GENE_WHITELIST: args += [ "-g", GENE_WHITELIST ]
if PATIENT_BLACKLIST: args += [ "-bp", PATIENT_BLACKLIST ]
if PATIENT_WHITELIST: args += [ "-p", PATIENT_WHITELIST ]
if NUM_MATRICES: args += [ "-n", NUM_MATRICES ]
# Use the permute_mutation_data module to generate the permuted matrices
P.run(P.parse_args(map(str, args)))
if __name__ == "__main__": run()
