null_model.py

#! /usr/bin/env python3

"""Association tests"""

import TopmedPipeline
import sys
import os
import subprocess
from time import localtime, strftime
from argparse import ArgumentParser
from copy import deepcopy
from shutil import copyfile
from datetime import datetime, timedelta

description = """
Association tests
"""

default_segment_length = "10000"

parser = ArgumentParser(description=description)
parser.add_argument("config_file", help="configuration file")
parser.add_argument("--cluster_type", default="UW_Cluster",
                    help="type of compute cluster environment [default %(default)s]")
parser.add_argument("--cluster_file", default=None,
                    help="json file containing cluster options")
parser.add_argument("-n", "--ncores", default="1",
                    help="number of cores to use; either a number (e.g, 1) or a range of numbers (e.g., 1-4) [default %(default)s]")
parser.add_argument("-e", "--email", default=None,
                    help="email address for job reporting")
parser.add_argument("--print_only", action="store_true", default=False,
                    help="print qsub commands without submitting")
parser.add_argument("--verbose", action="store_true", default=False,
                    help="enable verbose output to help debug")
parser.add_argument("--version", action="version",
                    version="TopmedPipeline "+TopmedPipeline.__version__,
                    help="show the version number and exit")
args = parser.parse_args()

configfile = args.config_file
cluster_file = args.cluster_file
cluster_type = args.cluster_type
ncores = args.ncores
email = args.email
print_only = args.print_only
verbose = args.verbose

version = "--version " + TopmedPipeline.__version__

cluster = TopmedPipeline.ClusterFactory.createCluster(cluster_type, cluster_file, verbose)

pipeline = cluster.getPipelinePath()
submitPath = cluster.getSubmitPath()
driver = os.path.join(submitPath, "runRscript.sh")

configdict = TopmedPipeline.readConfig(configfile)
configdict = TopmedPipeline.directorySetup(configdict, subdirs=["config", "data", "log", "report"])

# analysis init
cluster.analysisInit(print_only=print_only)

# null model
job = "null_model"

rscript = os.path.join(pipeline, "R", job + ".R")

config = deepcopy(configdict)
config["out_prefix"] = configdict["data_prefix"] + "_null_model"
config["out_phenotype_file"] = configdict["data_prefix"] + "_phenotypes.RData"
configfile = configdict["config_prefix"] + "_" + job + ".config"
TopmedPipeline.writeConfig(config, configfile)

submitID = cluster.submitJob(job_name=job, cmd=driver, args=[rscript, configfile, version], request_cores=ncores, email=email, print_only=print_only)


# null model report
job = "null_model_report"

rscript = os.path.join(pipeline, "R", job + ".R")

config = deepcopy(configdict)
config["out_prefix"] = configdict["out_prefix"] + "_null_model"
configfile = configdict["config_prefix"] + "_" + job + ".config"
TopmedPipeline.writeConfig(config, configfile)

submitID = cluster.submitJob(job_name=job, cmd=driver, args=[rscript, configfile, version], holdid=[submitID], email=email, print_only=print_only)

# post analysis
bname = "post_analysis"
job = "null_model" + "_" + bname
jobpy = bname + ".py"
pcmd=os.path.join(submitPath, jobpy)
argList = ["-a", cluster.getAnalysisName(), "-l", cluster.getAnalysisLog(),
           "-s", cluster.getAnalysisStartSec()]
cluster.submitJob(binary=True, job_name=job, cmd=pcmd, args=argList,
                  holdid=[submitID], print_only=print_only)