Python parseInputMutationModel Beispiele

Beispiel #1

Datei: genReads.py Projekt: meridith-e/neat-genreads

checkFileOpen(INPUT_VCF,'ERROR: could not open input VCF',required=False)
checkFileOpen(INPUT_BED,'ERROR: could not open input BED',required=False)
requiredField(OUT_PREFIX,'ERROR: no output prefix provided')
if (FRAGMENT_SIZE == None and FRAGMENT_STD != None) or (FRAGMENT_SIZE != None and FRAGMENT_STD == None):
	print '\nError: --pe argument takes 2 space-separated arguments.\n'
	exit(1)


"""************************************************
****             LOAD INPUT MODELS
************************************************"""


#	mutation models
#
MUT_MODEL = parseInputMutationModel(MUT_MODEL,1)
if CANCER:
	CANCER_MODEL = parseInputMutationModel(CANCER_MODEL,2)
if MUT_RATE < 0.:
	MUT_RATE = None

#	sequencing error model
#
if SE_RATE < 0.:
	SE_RATE = None
if SE_MODEL == None:
	print 'Using default sequencing error model.'
	SE_MODEL = SIM_PATH+'/models/errorModel_toy.p'
	SE_CLASS = ReadContainer(READLEN,SE_MODEL,SE_RATE)
else:
	# probably need to do some sanity checking

Beispiel #2

Datei: genReads.py Projekt: zstephens/neat-genreads

checkFileOpen(INPUT_VCF,'ERROR: could not open input VCF',required=False)
checkFileOpen(INPUT_BED,'ERROR: could not open input BED',required=False)
requiredField(OUT_PREFIX,'ERROR: no output prefix provided')
if (FRAGMENT_SIZE == None and FRAGMENT_STD != None) or (FRAGMENT_SIZE != None and FRAGMENT_STD == None):
	print '\nError: --pe argument takes 2 space-separated arguments.\n'
	exit(1)


"""************************************************
****             LOAD INPUT MODELS
************************************************"""


#	mutation models
#
MUT_MODEL = parseInputMutationModel(MUT_MODEL,1)
if CANCER:
	CANCER_MODEL = parseInputMutationModel(CANCER_MODEL,2)
if MUT_RATE < 0.:
	MUT_RATE = None

#	sequencing error model
#
if SE_RATE < 0.:
	SE_RATE = None
if SE_MODEL == None:
	print 'Using default sequencing error model.'
	SE_MODEL = SIM_PATH+'/models/errorModel_toy.p'
	SE_CLASS = ReadContainer(READLEN,SE_MODEL,SE_RATE)
else:
	# probably need to do some sanity checking