def main(): # 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.create_table('xchen_general', 'prot_refseq', 'prot_id INT, refseq_acc VARCHAR(100), PRIMARY KEY (refseq_acc)', '/isi/olga/xin/Halophile_project/db_source/prot2003-2014.tab', '\\t')
def main(argv): inputfile = '' try: opts, args = getopt.getopt(argv,"hi:",["ifile="]) except getopt.GetoptError: print ("test.py -i <inputfile>") sys.exit(2) for opt, arg in opts: if opt == '-h': print ("test.py -i <inputfile>") sys.exit() elif opt in ("-i", "--ifile"): inputfile = arg outputfile = open(outputdir, 'w') df = pd.read_table(inputdir, header = None, names=['reads','gi','ref'], delimiter = ' ') conn = connect(host = 'localhost', user = '******', passwd = 'f0029mc'); cursor = conn.cursor( cursors.DictCursor ); # sql = 'CREATE DATABASE IF NOT EXISTS rpoB_reads_assignment' # cursor.execute(sql) sql = 'USE xchen_projects' 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.create_table('prot_refseq', 'prot_id INT, refseq_acc VARCHAR(100), PRIMARY KEY (refseq_acc)', '/isi/olga/xin/Halophile_project/db_source/prot2003-2014.tab', '\t') cursor.close() conn.close()
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)