def options(argv):
global home, shareware, scr, scr_job, fasta_file, code, results, name, cleanup, task_id, no_homs
if len(argv) < 3:
usage()
sys.exit(2)
home = os.getcwd()
shareware = paths.join(home, "tools")
opts, args = getopt.getopt(argv, "t:p:cn")
code = args[0]
fasta_file = args[1]
results = args[2]
for o, a in opts:
if o == '-t':
id = '%(#)03d' % {"#": int(a)}
task_id = id
if o == '-p':
loadProps(a)
if o == '-c':
cleanup = False
if o == '-n':
no_homs = True
if task_id == None:
try:
id = '%(#)03d' % {"#": int(os.environ['PBS_ARRAYID']) - 1}
print "ID", id
task_id = id
except:
util.error("NO TASK ID")
name = "%s%s" % (code, task_id)
print code, " ", task_id, " ", name
try:
fasta_file = fasta_file.replace("%s", name)
except:
raise
results = paths.join(results, code, name)
scr_job = paths.join(scr, "jobs", name)
return
def options(argv):
global home, shareware,scr, scr_job, fasta_file, code, results, name, cleanup, task_id, no_homs
if len(argv) < 3:
usage()
sys.exit(2)
home = os.getcwd()
shareware = paths.join(home, "tools")
opts, args = getopt.getopt(argv, "t:p:cn")
code = args[0]
fasta_file = args[1]
results = args[2]
for o,a in opts:
if o == '-t':
id ='%(#)03d' % {"#": int(a)}
task_id = id
if o == '-p':
loadProps(a)
if o == '-c':
cleanup = False
if o == '-n':
no_homs = True
if task_id == None:
try:
id ='%(#)03d' % {"#": int(os.environ['PBS_ARRAYID'])-1}
print "ID",id
task_id = id
except:
util.error("NO TASK ID")
name = "%s%s" % (code, task_id)
print code," ",task_id," ",name
try:
fasta_file = fasta_file.replace("%s", name)
except:
raise
results = paths.join(results, code, name)
scr_job = paths.join(scr, "jobs", name)
return
def existsOrFail(path):
if not os.path.exists(path):
from hpf.utilities import error
error( "Path doesn't exist: %s" % path, path)
return path