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)
