def main(argv): inputfile = '' outputfile = '' # try: # opts, args = getopt.getopt(argv,"hi:o:",["ifile=","ofile="]) # except getopt.GetoptError: # print ("test.py -i <inputfile> -o <outputfile>") # sys.exit(2) # for opt, arg in opts: # if opt == '-h': # print ("test.py -i <inputfile> -o <outputfile>") # sys.exit() # elif opt in ("-i", "--ifile"): # inputfile = arg # elif opt in ("-o", "--ofile"): # outputfile = arg try: opts, args = getopt.getopt(argv,"ho:",["ofile="]) except getopt.GetoptError: print ("test.py -o <onputfile>") sys.exit(2) for opt, arg in opts: if opt == '-h': print ("test.py -o <onputfile>") sys.exit() elif opt in ("-o", "--ofile"): outputfile = arg # sql = 'CREATE DATABASE IF NOT EXISTS rpoB_reads_assignment' # cursor.execute(sql) #sql = 'SELECT reads_name, sequence FROM reads_trimmed_merged.DS2_1_trimmed_merged_fa WHERE id < 100 AND SUBSTRING(reads_name, 2) NOT IN (SELECT reads_name from reads_assignment.DS2_1_assignment);' sqlfun = SQLfunc() sqlfun.fetch_seq_exclude("xchen_projects", "SS37_trimmed_fa", "blastn_SS37_reads_taxa_tmp", outputfile)