#!/usr/bin/env python
from omics_pipe.parameters.default_parameters import default_parameters
from omics_pipe.utils import *
p = Bunch(default_parameters)
[docs]def intogen(sample, intogen_flag):
'''Runs Intogen to rank mutations and implication for cancer phenotype. Follows variant calling.
input:
.vcf
output:
variant list
citation:
Gonzalez-Perez et al. 2013. Intogen mutations identifies cancer drivers across tumor types. Nature Methods 10, 1081-1082.
link:
http://www.intogen.org/
parameters from parameter file:
VCF_FILE:
INTOGEN_OPTIONS:
INTOGEN_RESULTS:
INTOGEN_VERSION:
USERNAME:
WORKING_DIR:
TEMP_DIR:
SCHEDULER:
VARIANT_RESULTS:
'''
#vcf_file = p.SNPIR_RESULTS + "/" +sample + "/final_variants.vcf"
spawn_job(jobname = 'intogen', SAMPLE = sample, LOG_PATH = p.LOG_PATH, RESULTS_EMAIL = p.RESULTS_EMAIL, SCHEDULER = p.SCHEDULER, walltime = "240:00:00", queue = p.QUEUE, nodes = 1, ppn = 8, memory = "29gb", script = "/intogen_drmaa.sh", args_list = [p.VCF_FILE, p.INTOGEN_OPTIONS, p.INTOGEN_RESULTS, p.INTOGEN_VERSION, p.USERNAME, p.WORKING_DIR, p.TEMP_DIR, sample, p.SCHEDULER, p.VARIANT_RESULTS])
job_status(jobname = 'intogen', resultspath = p.INTOGEN_RESULTS, SAMPLE = sample, outputfilename = sample + "/variant_genes.tsv", FLAG_PATH = p.FLAG_PATH)
return
if __name__ == '__main__':
intogen(sample, intogen_flag)
sys.exit(0)