in src/main/scripts/rna_expression_fastq.py [0:0]
def parse_arguments(script_name, argv):
species = None
read_type = None
job_name = None
dir_out = None
fastq_list = None
fastq_list_r2 = None
cufflinks_library_type = None
library_type = None
project = None
run = None
toolset = None
flag_xenome = None
cores_per_sample = None
genome_load = None
sync = None
master_mode = None
verbose = None
sample_name_list = None
try:
opts, args = getopt.getopt(argv, "hs:t:j:d:f:q:c:l:p:r:n:x:k:g:i:v", ["help", "species=", "read_type=",
"job_name=", "dir_out=", "fastq_list=",
"fastq_list_r2",
"cufflinks_library_type=",
"library_type=", "project=", "run=",
"toolset=", "flag_xenome=",
"cores_per_sample=", "genome_load=",
"sync=", "sample_name_list", "master_mode",
"verbose"])
for opt, arg in opts:
if opt == '-h':
print(script_name + ' -s <species> -t <read_type> -j <job_name> -d <dir_out> -f <fastq_list> '
'-q <fastq_list_r2> -c <cufflinks_library_type> -l <library_type> -p <project> '
'-r <run> -n <toolset> -x <flag_xenome> -k <cores_per_sample> -g <genome_load> '
'<sync> -i <sample_name_list> <master_mode> -v <verbose>')
sys.exit()
elif opt in ("-s", "--species"):
species = arg
elif opt in ("-t", "--read_type"):
read_type = arg
elif opt in ("-j", "--job_name"):
job_name = arg
elif opt in ("-d", "--dir_out"):
dir_out = arg
elif opt in ("-f", "--fastq_list"):
fastq_list = arg
elif opt in ("-q", "--fastq_list_r2"):
fastq_list_r2 = arg
elif opt in ("-c", "--cufflinks_library_type"):
cufflinks_library_type = arg
elif opt in ("-l", "--library_type"):
library_type = arg
elif opt in ("-p", "--project"):
project = arg
elif opt in ("-r", "--run"):
run = arg
elif opt in ("-n", "--toolset"):
toolset = arg
elif opt in ("-x", "--flag_xenome"):
flag_xenome = arg
elif opt in ("-k", "--cores_per_sample"):
cores_per_sample = arg
elif opt in ("-g", "--genome_load"):
genome_load = arg
elif opt in "--sync":
sync = arg
elif opt in "--master_mode":
master_mode = True
elif opt in ("-v", "--verbose"):
verbose = 'True'
elif opt in ("-i", "--sample_name_list"):
sample_name_list = arg
if not species:
print('Species (-s <species>) is required')
usage()
sys.exit(2)
if not read_type:
print('Read type (-t <read_type>) is required')
usage()
sys.exit(2)
if not fastq_list:
print('The path to the input manifest fastq file (-f <fastq_list>) is required')
usage()
sys.exit(2)
if not dir_out:
print('The output directory for the analysis (-d <dir_out>) is required')
usage()
sys.exit(2)
if not cufflinks_library_type:
print('The cufflinks library type (-c <cufflinks_library_type>) is required')
usage()
sys.exit(2)
if not toolset:
print('The set of tools (-n <toolset>) is required')
usage()
sys.exit(2)
return species, read_type, job_name, dir_out, fastq_list, fastq_list_r2, cufflinks_library_type, library_type, \
project, run, toolset, flag_xenome, cores_per_sample, verbose, sync, genome_load, sample_name_list, \
master_mode
except getopt.GetoptError:
usage()
sys.exit(2)