Esempi in Python per checkFileOpen

Esempio n. 1

File: genReads.py Progetto: meridith-e/neat-genreads

	MYJOB = 1
	NJOBS = 1
SAVE_NON_N = args.nnr

RNG_SEED = args.rng
if RNG_SEED == -1:
	RNG_SEED = random.randint(1,99999999)
random.seed(RNG_SEED)


"""************************************************
****            INPUT ERROR CHECKING
************************************************"""


checkFileOpen(REFERENCE,'ERROR: could not open reference',required=True)
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
#

Esempio n. 2

File: genReads.py Progetto: zstephens/neat-genreads

	MYJOB = 1
	NJOBS = 1
SAVE_NON_N = args.nnr

RNG_SEED = args.rng
if RNG_SEED == -1:
	RNG_SEED = random.randint(1,99999999)
random.seed(RNG_SEED)


"""************************************************
****            INPUT ERROR CHECKING
************************************************"""


checkFileOpen(REFERENCE,'ERROR: could not open reference',required=True)
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
#