def indexing_ref(index_cmd, db, ref_in_fasta, logger) : """ index the give reference """ make_dir_if_not_exist(dirname(db)) print index_subprogram index_cmd += "%s -p %s %s" %(index_subprogram, db, ref_in_fasta) run(index_cmd, logger)
# get mapping program #
mapper_prog = params["PROGRAM"]
# get command line default setting #
default_combo_dict = {}
for customized_combo, default_setting in params["DEFAULT_SETTING"].iteritems() :
default_combo_dict[customized_combo] = default_setting
# get output info #
out_root_dir = params["OUTPUT_FOLDER"]
dated_output = int(params["DATED_OUTPUT"]) # this creates timestamped subfolders under the out_root_dir if set True #
structure = params["STRUCTURE"]
if dated_output :
out_root_dir = join(out_root_dir, time_stamper())
make_dir_if_not_exist(out_root_dir)
# get indexing info #
ref_db, ref_fasta, skip, index_subprogram = "", "", -1, ""
for k, v in params["INDEXING"].iteritems() :
if k == "DB" :
ref_db = v
elif k == "FASTA" :
ref_fasta = v
elif k == "SKIP" :
skip = v
elif k == "SUBPROGRAM" :
index_subprogram = mapper_prog + " %s" %(v)
if not skip :
check_file_existence(logger, debug, ref_fasta)
indexing_ref(index_subprogram, ref_db, ref_fasta, logger)
