in src/main/scripts/dna_capture_var_fastq.py [0:0]
def parse_arguments(script_name, argv):
species = None
read_type = None
genome = None
targeted_kit = None
job_name = None
dir_out = None
fastq_list = None
fastq_list_r2 = None
library_type = None
project = None
run = None
toolset = None
flag_xenome = None
cores_per_sample = None
sync = None
master_mode = None
verbose = None
sample_name_list = None
novoalign_tune = None
try:
opts, args = getopt.getopt(argv, "hs:t:g:k:j:d:f:q:l:p:r:n:x:c:i:a:v", ["help", "species=", "read_type=",
"genome=", "targeted_kit=", "job_name=",
"dir_out=", "fastq_list=",
"fastq_list_r2", "library_type=",
"project=", "run=",
"toolset=", "flag_xenome=",
"cores_per_sample=", "sync=",
"sample_name_list", "novoalign_tune",
"master_mode", "verbose"])
for opt, arg in opts:
if opt == '-h':
print(script_name + ' -s <species> -t <read_type> -g <genome> -k <targeted_kit> -j <job_name> '
'-d <dir_out> -f <fastq_list> -q <fastq_list_r2> -l <library_type> -p <project> '
'-r <run> -n <toolset> -x <flag_xenome> -c <cores_per_sample> <sync> '
'-i <sample_name_list> -a <novoalign_tune> <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 ("-g", "--genome"):
genome = arg
elif opt in ("-k", "--targeted_kit"):
targeted_kit = 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 ("-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 ("-c", "--cores_per_sample"):
cores_per_sample = 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
elif opt in ("-a", "--novoalign_tune"):
novoalign_tune = 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 toolset:
print('The set of tools (-n <toolset>) is required')
usage()
sys.exit(2)
if not targeted_kit:
print('The targeted kit name (-k <targeted_kit>) is required')
usage()
sys.exit(2)
return species, read_type, job_name, dir_out, fastq_list, fastq_list_r2, library_type, project, run, toolset, \
flag_xenome, cores_per_sample, verbose, sync, genome, targeted_kit, sample_name_list, master_mode, \
novoalign_tune
except getopt.GetoptError:
usage()
sys.exit(2)