# verify inputs, print to screen and log
(infile_pass, infile_msg) = ic.CheckInfile(args.infile)
(config_pass, config_msg) = ic.CheckConfig(args.configfile)
verify_msg = infile_msg + '\n' + config_msg
pipelineHelpers.LogInputCheck(verify_msg)
if not (infile_pass and config_pass):
raise Exception('Invalid input.')
pipeline_msg = '\n---------------------------------\n' \
'Running pipeline\n' \
'---------------------------------'
print pipeline_msg
log = pipelineHelpers.GetLogFile('MAIN')
pipelineHelpers.Logging('INFO', log, pipeline_msg)
num_procs = line_count * 4
if( args.phase):
if(not args.splitbams):
pipeline_run([pipeline.find_roi_bam], multiprocess=num_procs, verbose=1)
if(args.cnvDelFile):
pipeline_run([pipeline.complete_pipeline])
else:
pipeline_run([pipeline.complete_pipeline_gain])
else:
params.SetSplitBamsPath(args.splitbams)
import os
import random
from helpers import pipelineHelpers
from ruffus import *
import logging, sys
from re import sub
import taskHelpers
from itertools import izip
import itertools
import re
import subprocess
global bases
bases = ('A','T','C','G')
log = pipelineHelpers.GetLogFile('Bamgineer')
import utils
import vcf
import gzip
import shutil
chr_list = range(1,23)
event_list=['gain','loss']
sentinel_path, results_path,haplotype_path,cancer_dir_path,tmpbams_path,finalbams_path = taskHelpers.GetProjectNamePathRunID()
def initPool(queue, level, terminating_):
"""
This causes the logging module to be initialized with the necessary info
in pool threads to work correctly.
"""
import os
import sys
from re import sub
from ruffus import *
from helpers import depthOfCoverageTasks, depthOfCoverageHelpers, pipelineHelpers
from helpers import runIDHelpers as rid
from helpers import parameters as params
import subprocess
current_path = params.GetProgramPath()
log = pipelineHelpers.GetLogFile('DepthOfCoverage')
def runCommand(cmd):
try:
process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stdin=subprocess.PIPE, shell=True)
stdout, stderr = process.communicate()
except OSError as e:
print("Execution failed:", e)