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main and config changes #4

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180 changes: 101 additions & 79 deletions docker-controlfreec/controlFreeq_wrap_final.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@
import os
import sys
import time
import logging
import argparse
import traceback
import ConfigParser

from time import strftime, gmtime
Expand All @@ -26,15 +26,9 @@
if not os.path.isdir(logPath):
os.makedirs(logPath)

# set output path
outputPath = pgmPath + '/output'
if not os.path.isdir(outputPath):
os.makedirs(outputPath)



###############################################################################
######### Log file and time stamp
######### Create file objects
###############################################################################

#create time stamp YYMMDD_HH:MM:SS (Greenwhich mean time)
Expand All @@ -50,44 +44,51 @@

newUser = "#####################################################################"

#Create conneciton to log file
#Create connection to log file
try:
pywrapLog = open(os.path.join(logPath, logFile), 'a')
pywrapLog.write('\n'+newUser+'\n'+logStamp + "--Successfully opened log file")
pywrapLog.write('\n'+newUser+'\n'+logStamp + "-- Successfully opened log file")
except:
pywrapLog.write('\n'+logStamp + 'Invalid pathname, or invalid user permissions\n')
raise IOError('Invalid pathname, or invalid user permissions')


###############################################################################
######### Define Arguments
######### Classes and functions
###############################################################################

# Create function for UNcaught exceptions
def catchExceptions(exctype, value, tb):
pywrapLog.write('\n'+logStamp+'-- '+'UNCAUGHT ERROR')
exctype = str(exctype)
pywrapLog.write('\n'+'TYPE: ' + exctype)
pywrapLog.write('\n'+'VALUE: ' + str(value))
tb = traceback.extract_tb(tb)
pywrapLog.write('\n'+'TRACEBACK: '+'\n')
for item in tb:
pywrapLog.write(str(item))
pywrapLog.write('> \n')


# Override excepthook; will return uncaught exceptions in catchExceptions
sys.excepthook = catchExceptions

parser = argparse.ArgumentParser('Support script for ControlFREEQ client')

# REQUIRED
# REQUIRED
parser.add_argument('--runId', type=str, required=True)
# check for file
parser.add_argument('--input', type=str, required=True)
parser.add_argument('--control', type=str, required=True)

# check for directory
parser.add_argument('--input', type=file, required=True)
parser.add_argument('--control', type=file, required=True)
parser.add_argument('--chrPath', type=str, required=True)
# output path create if not there
parser.add_argument('--outputPath', type=str, required=True)

# check for file
parser.add_argument('--bed', type=str, required=True)
parser.add_argument('--bed', type=file, required=True)

# OPTIONAL
parser.add_argument('--step', type=int, default=250, required=False)
parser.add_argument('--intercept', type=int, default=0, required=False)
parser.add_argument('--threads', type=int, default=1, required=False)
parser.add_argument('--minDepth', type=int, default=50, required=False)


# if 0 don't include in parameters
parser.add_argument('--contamination', type=int, default=0)
parser.add_argument('--contamination', type=int, default=0, required=False)


###############################################################################
Expand All @@ -96,63 +97,84 @@


def main(*args):

# try:
# try:
print "here"
args = parser.parse_args()
try:
config = ConfigParser.ConfigParser()

configFile = str(args.runId + '.config')

pywrapConfig = open(args.outputPath + configFile, 'wb')
pywrapLog.write('\n'+logStamp + "--Successfully opened config file")

config.add_section('general')
config.add_section('sample')
config.add_section('control')
config.add_section('BAF')
config.add_section('target')


except IOError:
pywrapLog.write('\n'+logStamp + 'Invalid pathname, or invalid user permissions\n')
raise IOError('Invalid pathname, or invalid user permissions')

pywrapLog.write('\n'+logStamp + "--Successfully passed arguments\n")

config.set('general', 'chrLenFile', '/mnt/data/hg19.len')
config.set('general', 'window', '1000'+'\n')

config.set('general', 'step', args.step)
config.set('general', 'ploidy', '2')
config.set('general', 'chrFiles', str(args.chrPath)+'\n')

config.set('general', 'intercept', args.intercept)
config.set('general', 'minMappabilityPerWindow', '0.7'+'\n')

config.set('general', 'outputDir', str(args.outputPath) + '\n')

config.set('general', 'breakPointType', '4')
config.set('general', 'maxThreads', '4')
config.set('general', 'readCountThreshold', '50' + '\n')

config.set('general', 'contaminationAdjustment', 'True')
config.set('general', 'contamination', '65')

config.set('sample', 'mateFile', args.input)
config.set('sample', 'inputFormat', 'SAM')
config.set('sample', 'mateOrientation', '0')

config.set('control', 'mateFile', args.control)
config.set('control', 'inputFormat', 'SAM')
config.set('control', 'mateOrientation', '0')
try:
try:

args = parser.parse_args()

# check for outputPath directory; if not, then create
if not os.path.isdir(args.outputPath):
os.makedirs(args.outputPath)

# check for chrPath directory; if not, then create
if not os.path.isdir(args.chrPath):
os.makedirs(args.chrPath)

try:
config = ConfigParser.ConfigParser()

configFile = str(args.runId + '.config')

pywrapConfig = open(args.outputPath + configFile, 'wb')
pywrapLog.write('\n'+logStamp + "-- Successfully opened config file")

config.add_section('general')
config.add_section('sample')
config.add_section('control')
config.add_section('BAF')
config.add_section('target')


except IOError:
pywrapLog.write('\n'+logStamp + 'Invalid pathname, or invalid user permissions\n')
raise IOError('Invalid pathname, or invalid user permissions')

pywrapLog.write('\n'+logStamp + "-- Successfully passed arguments\n")

config.set('general', 'chrLenFile', '/mnt/data/hg19.len')
config.set('general', 'window', '1000'+'\n')

config.set('general', 'step', args.step)
config.set('general', 'ploidy', '2')
config.set('general', 'chrFiles', str(args.chrPath)+'\n')

config.set('general', 'intercept', args.intercept)
config.set('general', 'minMappabilityPerWindow', '0.7'+'\n')

config.set('general', 'outputDir', str(args.outputPath) + '\n')

config.set('general', 'breakPointType', '4')
config.set('general', 'maxThreads', '4')
config.set('general', 'readCountThreshold', '50' + '\n')

config.set('general', 'contaminationAdjustment', 'True')
if not args.contamination == 0:
config.set('general', 'contamination', args.contamination)

config.set('sample', 'mateFile', args.input)
config.set('sample', 'inputFormat', 'SAM')
config.set('sample', 'mateOrientation', '0')

config.set('control', 'mateFile', args.control)
config.set('control', 'inputFormat', 'SAM')
config.set('control', 'mateOrientation', '0')

config.set('target', 'captureRegions', args.bed)



# write to config file
config.write(pywrapConfig)

except:
raise
except:
raise
return 2
return 0

config.set('target', 'captureRegions', args.bed)

config.write(pywrapConfig)
return 0

###############################################################################
######### Run
Expand Down