def create_setting_from_file(cls, args):
"""
TODO: switch between assembler(genovo/xgenovo)+glimmer+blast and MINE
ignore metasim for now
do we need assembler(genovo/xgenovo)+glimmer+blast+MINE?
"""
# print type(args.control_file), dir(args.control_file)
# print args.control_file.closed, args.control_file.name
try:
if args.control_file is "control":
print "Use control file at ./control"
# args.control_file = "control"
control_file = os.path.abspath(args.control_file)
path_utils.check_file(control_file)
all_pars = parse_control_file2(control_file)
if args.sub_command == "process":
print "Subcommand: process"
infile = os.path.abspath(args.infile)
wdir = os.path.dirname(infile)
path_utils.check_file(infile)
path_utils.check_directory(wdir)
setting = cls(wdir=wdir)
if "genovo_pdir" in all_pars and "xgenovo_pdir" in all_pars:
raise NameError("Error!! both genovo_pdir and xgenovo_pdir exist in the control file.")
if "genovo_pdir" in all_pars:
assembler_pdir_full = os.path.abspath(os.path.expanduser(all_pars["genovo_pdir"]))
assembler_prog = "genovo"
elif "xgenovo_pdir" in all_pars:
assembler_pdir_full = os.path.abspath(os.path.expanduser(all_pars["xgenovo_pdir"]))
assembler_prog = "xgenovo"
else:
raise NameError("Error! No assembler specified! genovo_pdir or xgenovo_pdir is required")
glimmer_pdir_full = os.path.abspath(os.path.expanduser(all_pars["glimmer_pdir"]))
blast_pdir_full = os.path.abspath(os.path.expanduser(all_pars["blast_pdir"]))
blast_db_full = os.path.abspath(os.path.expanduser(all_pars["blast_db"]))
path_utils.check_directory(assembler_pdir_full)
path_utils.check_directory(glimmer_pdir_full)
path_utils.check_directory(blast_pdir_full)
# path_utils.check_directory(blast_db_full)
setting.add_all(
assembler_infile=infile,
assembler_prog=assembler_prog,
assembler_pdir=assembler_pdir_full,
glimmer_pdir=glimmer_pdir_full,
blast_pdir=blast_pdir_full,
blast_db=blast_db_full
)
setting.check_parameters_program(assembler_prog)
setting.check_parameters_program("glimmer")
setting.check_parameters_program("blast")
setting._set_master_file_tag()
elif args.sub_command == "summary":
print "Subcommand: summary "
csv_dir = os.path.abspath(args.csv_dir) # wdir
path_utils.check_directory(csv_dir)
wdir = csv_dir
setting = cls(wdir=wdir, run_mine=True)
mine_pdir_full = os.path.abspath(os.path.expanduser(all_pars["mine_pdir"]))
# infile = path_utils.check_wdir_prefix(all_pars["wdir"], )
infile = setting.generate_default_outfile_name(args.mine_infile, ".csv")
infile = os.path.abspath(infile) # #FIXME, should be able to do it better
csv_list = []
for name in glob.glob(wdir + '/*.csv'):
if name.find(args.mine_infile) > 0:
continue
if name.find("Results.csv") > 0 :
continue
if name.find("tmp.csv") > 0 :
continue
print "Found CSV file: ", name
csv_list.append(name)
print "Total: %d CSV files in %s.\nPlease remove unwanted *.csv file and restart." % (len(csv_list), wdir)
setting.add_all(
mine_pdir=mine_pdir_full,
mine_infile=infile,
csv_files=csv_list,
mine_overwrite=args.mine_overwrite
)
setting.check_parameters_program("mine")
except KeyError as e:
# raise KeyError("Missing essential setting", e)
print "ERROR: Missing essential setting %s in control file:%s" % (e, control_file)
if args.debug > 1:
raise
sys.exit(5)
except IOError as e:
print e
if args.debug > 1:
raise
sys.exit(6)
# keys = controlfile.all_arguments.keys()
# print keys
for parameter in list_all_optionals:
if parameter in all_pars.keys():
if args.debug > 0:
print "ADDING: ", parameter, all_pars[parameter]
setting.add(parameter, all_pars[parameter])
setting.print_all(args.debug)
return setting
def check_file_exist(self, filename, check_exist):
warnings.warn("Deprecated method ", DeprecationWarning)
if check_exist:
path_utils.check_file(filename)
